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DOE OSTI2022

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relies on the physical separation of the Ab/Ag complex in equilibrium molecular dynamics (MD) simulations, (ii) a collection of 18 scoring functions that act on an ensemble of structures created using homology modeling software, and (iii) methods based on the molecular mechanics-generalized Born surface area (MM-GBSA) energy decomposition, in which the individual contributions of the energy terms are scaled to optimize agreement with the experiment. When applied to a set of 49 antibody mutations in two Ab/HIV gp120 complexes, all of the methods are found to have modest accuracy, with the highest Pearson correlations reaching about 0.6. In particular, the most computationally intensive method, i.e., MD simulation, did not outperform several scoring functions. The optimized energy decomposition methods provided marginally higher accuracy, but at the expense of requiring experimental data for parametrization. Within each method class, we examined the effect of the number of independent computational replicates, i.e., modeled structures or reinitialized MD simulations, on the prediction accuracy. We suggest using about ten modeled structures for scoring methods, and about five simulation replicates for MD simulations as a rule of thumb for obtaining reasonable convergence. We anticipate that our study will be a useful resource for practitioners working to incorporate binding affinity calculations within their protein design and optimization process.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Evidence for Environmental Stripping in the Coma Cluster

The stability and longevity of globular clusters (GCs) make them effective tracers of the dynamical histories of galaxies in cluster environments. We construct a catalog of 23,351 GC candidates in the Coma Cluster using imaging from the Hubble Space Telescope Advanced Camera for Surveys. We cross-match galaxy data from the SIMBAD, NASA/IPAC Extragalactic Database, and Sloan Digital Sky Survey archives to construct a galaxy sample and model their GC populations using the GC specific frequency. We find several galaxies with significantly smaller GC populations than expected from their luminosities, consistent with either tidal stripping or intrinsically low formation efficiencies. We analyze annular and Voronoi GC radial profiles of the two brightest cluster galaxies (BCGs), NGC 4874 and NGC 4889, as well as other Coma galaxies. A two-dimensional Voronoi density mapping reveals GC populations with marked deficits compared to our modeled expectations, including galaxies in proximity to the BCGs (e.g., IC 3998, NGC 4875, and NGC 4876) and others distributed across Coma (e.g., NGC 4908, NGC 4883, and IC 4042). Azimuthal symmetry testing suggests past dynamical interactions may have truncated GC systems in some galaxies, while intrinsic deficits are probable in others (e.g., IC 3973, IC 3976, IC 4040, and IC 4045). Our results show that GC deficits exist in several Coma galaxies and that the two-dimensional density structure reveals environmental signatures, with asymmetry statistics consistent with directional stripping. These findings highlight GC populations as powerful probes of environmental processing and the dynamical histories of galaxies in dense cluster environments.

Pomeroy, Richard T. [University of Texas Rio Grand↗

DOE OSTI2019

Unsupervised discovery of temporal sequences in high-dimensional datasets, with applications to neuroscience

Identifying low-dimensional features that describe large-scale neural recordings is a major challenge in neuroscience. Repeated temporal patterns (sequences) are thought to be a salient feature of neural dynamics, but are not succinctly captured by traditional dimensionality reduction techniques. Here, we describe a software toolbox—called seqNMF—with new methods for extracting informative, non-redundant, sequences from high-dimensional neural data, testing the significance of these extracted patterns, and assessing the prevalence of sequential structure in data. We test these methods on simulated data under multiple noise conditions, and on several real neural and behavioral data sets. In hippocampal data, seqNMF identifies neural sequences that match those calculated manually by reference to behavioral events. In songbird data, seqNMF discovers neural sequences in untutored birds that lack stereotyped songs. Thus, by identifying temporal structure directly from neural data, seqNMF enables dissection of complex neural circuits without relying on temporal references from stimuli or behavioral outputs.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Development of Large Scale Extrusion Deposition for Structural Applications

Large Scale Extrusion Deposition (LSED) is an evolving additive manufacturing (AM) technology that research, such as that taking place at Oak Ridge National Laboratory (ORNL) and companies like Local Motors, are continuing to utilize and develop new applications. A major LSED application of interest has been molds and tooling as it allows for much shorter production time and lower cost. However, interest has been expanding into using LSED for more structural applications due to more frequent use of high performing polymer composites as feedstock. The use of LSED for structural applications is of particular interest to Local Motors as it is currently being used to create commercially viable, energy efficient electric vehicles. LSED offers a unique opportunity when compared to traditional manufacturing methods as it can significantly reduce the number of components necessary, while decreasing embodied energy and carbon emissions. Even with these benefits however, it is important that LSED is properly understood from a structural aspect as this field has not been as heavily researched as tooling. To ensure a high level of safety and repeatability is an essential responsibility of a manufacturer whose products are structural in nature. As such it is important to understand the materials and LSED process to make structural objects that the manufacturer can be confident in. The main goals of this project were to: develop and investigate materials that are of interest for structural LSED applications, further develop and understand the current machines used in LSED and develop simulations tools of LSED and the mechanical properties of the created structure. Material development focused on composite materials that have high mechanical properties and are stable in a variety of environments. The materials were tested to determine their as printed mechanical and thermal properties as these are necessary for simulations. Once the materials were investigated thoroughly, it allowed for simulations to be performed to compare to experimental data with simulations. Materials were also vetted to determine candidates for multi-material printing. The machine development focused around the areas of process monitoring, non-destructive evaluation, and quality control. Finally, the goal of the simulations was to develop a realistic model of printed structures, including in-process simulation and dynamic simulation. The routes to get to some of these goals and the depth in which they were investigated changed throughout the project due to personnel changes and the COVID-19 pandemic. This project resulted in many valuable results such as the development of an nondestructive evaluation (NDE) technique for interlayer defects, proof of simulation for warpage in simple parts, the development and utilization of a profilometer to monitor a print for defects or inconsistencies, thorough investigation of a material used commercially for structural LSED applications and valuable experimental data on the applicability and advantages of multi-material crush structures versus their neat counterparts by creation and testing of samples.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Dynamic responses of submerged components in advanced reactors: experimental and numerical studies

The seismic design of an advanced nuclear reactor must consider the interaction of vessel internal components with the surrounding coolant: fluid–structure interaction (FSI). Available analytical solutions for FSI of submerged components do not accommodate multiple-component, intense seismic inputs and complex reactor and internal geometries. Physical testing of reactor vessels and internals to inform seismic design is impractical and cost-prohibitive, leaving the use of verified and validated, robust numerical models as the only plausible option for analysis and design. Physical data that could be used for validating such numerical models for multi-component shaking are not available. This article describes an experimental program performed on a 6-degree-of-freedom earthquake simulator to generate data that could support validation of seismic FSI numerical models for submerged components in commercial finite element codes. A scaled model of a base-supported reactor vessel with simplified representations of submerged internals was tested to generate submerged-component response histories for a range of seismic inputs. The generated data were used to validate numerical models in the finite element code LS-DYNA. Numerical models were validated for calculation of hydrodynamic pressure responses on internals, in-water frequencies of internals, and acceleration responses of internals. The generated data and the analysis recommendations could aid engineering analysts designing submerged components and systems for seismic effects.

Engineering↗

DOE OSTI2026

Toward Intelligent Multimodal Holography for Real-Time Chemical Imaging of Dynamic Ion Separation

Molecular-level visualization of ion transport and separation dynamics in complex environments is crucial for advancing energy systems, water purification, and critical materials recovery. Achieving this requires imaging platforms that combine structural sensitivity, chemical specificity, and real-time operation. Digital off-axis holography (DOAH) provides high-throughput, label-free quantitative phase imaging but inherently lacks chemical selectivity. Integrating DOAH with complementary spectroscopic channels such as fluorescence or hyperspectral imaging introduces the needed molecular specificity, while also creating challenges in multimodal data fusion, synchronization, and computational throughput. Artificial intelligence offers a powerful route to address these limitations by uniting physics-based reconstruction with data-driven interpretation. In this Perspective, we outline a framework for intelligent multimodal holography and demonstrate its potential using a preliminary AI-driven test case. Raw DOAH holograms of lanthanide solutions subjected to magnetic field gradients were analyzed using multi-agent AI workflows that autonomously selected reconstruction tools, extracted NMF components, and generated scientific claims consistent with true paramagnetic and diamagnetic behavior. This demonstration shows how AI-enabled reasoning can deliver real-time chemical–structural interpretation directly from raw holograms. Together, these advances define a path toward adaptive, intelligent holography platforms capable of supporting in situ chemical separations, dynamic ion transport analysis, and next-generation interfacial science.

Ricchiuti, Giovanna↗

DOE OSTI2023

Abbreviated Technical Report: Experimentally Interrogating Detonation Chemistry on Sub-Nanosecond to Nanosecond Timescales

Direct experimental measurement of chemical reactions during high explosive detonation remains challenging. Theory and modeling have long preceded experiment in the fundamental physical and chemical kinetic properties of detonation, and experimentation at the relevant timescales are needed to both validate models and provide fundamental understanding of detonation. In this LDRD-ER project, two approaches, x-ray diffraction and core-level x-ray Raman, were developed and used to further experimental capabilities to address this gap. We further developed dynamic x-ray diffraction to directly detect nanodiamond formation during detonation, providing experimental data towards resolving longstanding controversy in the scientific literature, and although the full kinetics have not yet been fully mapped, diamond diffraction appears on the same timescales as detonation soot formation. In the second research thrust, we have developed core-level x-ray Raman for use with high explosives. This technique provides information analogous to x-ray absorption spectroscopy and electron energy loss spectroscopy, but uses inelastic scattering of hard x-rays that can interrogate chemistry around light elements much deeper into the material. The low cross section and requisite high solid angle collection have hindered its use for ultra-fast spectroscopy. We developed and tested a high-q spectrometer which will substantially increase cross section and signal-to-noise, showing this method will also not dramatically alter, compared to x-ray absorption, the most discriminating spectral features of C, N, and O from various high explosives and expected detonation products. We have also used x-ray Raman combined with OCEAN electronic structure calculations to explore dynamic photodegradation mechanisms in PETN and CL-20 explosives. This provides a pathway towards implementing capability to dynamically explore chemistry at an x-ray free electron laser.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Deuteron off-resonance rotating frame relaxation for the characterization of slow motions in rotating and static solid-state proteins

Here, we demonstrate the feasibility of deuterium solid-state NMR off-resonance rotating frame relaxation measurements for studies of slow motions in biomolecular solids. The pulse sequence, which includes adiabatic pulses for magnetization alignment, is illustrated for static and magic-angle spinning conditions away from rotary resonances. We apply the measurements for three systems with selective deuterium labels at methyl groups: a) a model compound, Fluorenylmethyloxycarbonyl methionine-D 3 amino acid, for which the principles of the measurements and corresponding motional modeling based on rotameric interconversions are demonstrated; b) amyloid-β 1-40 fibrils labeled at a single alanine methyl group located in the disordered N-terminal domain. This system has been extensively studied in prior work and here serves as a test of the method for complex biological systems. The essential features of the dynamics consist of large-scale rearrangements of the disordered N-terminal domain and the conformational exchange between the free and bound forms of the domain, the latter one due to transient interactions with the structured core of the fibrils. and c) a 15-residue helical peptide which belongs to the predicted α-helical domain near the N-terminus of apolipoprotein B. The peptide is solvated with triolein and incorporates a selectively labeled leucine methyl groups. The method permits model refinement, indicating rotameric interconversions with a distribution of rate constants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Structural Impact of Grid-Forming Inverters on Power System Coherency

This paper addresses the following fundamental research question: how does the integration of grid-forming inverters (GFMs) replacing conventional synchronous generators (SGs) impact the slow coherent eigen-structure and the low frequency oscillatory behavior of future power systems? Due to time-scale separated dynamics, generator states inside a coherent area synchronize over a fast time-scale due to stronger coupling, while the areas themselves synchronize over a slower time scale. Our mathematical analysis shows that due to the large-scale integration of GFMs, the weighted Laplacian structure of the frequency dynamics is preserved, however, the entries of the Laplacian may be significantly modified based on the location and penetration levels of the GFMs. This can impact and potentially significantly alter the coherency structure of the system. We have validated our findings with numerical results using the IEEE 68-bus test system.

Mukherjee, Sayak [BATTELLE (PACIFIC NW LAB)]↗

DOE OSTI2020

Large-scale inflatable structures for tunnel protection: a review of the Resilient Tunnel Plug project

The protection of underground civil infrastructure continues to be a high priority for transportation and transit security agencies. In particular, rail transit tunnels running under bodies of water are susceptible to disruptions due to flooding caused by extraordinary climatic events such as hurricanes or other events resulting from human activities. Several events have taken place in the past decades that have demonstrated the need to mitigate vulnerabilities or, at least, minimize the consequences of catastrophic events. Although it is impossible to prevent all situations that can lead to flooding, damage can be substantially decreased by reducing the area affected by the event. To minimize the effects of an event, a possible approach is to compartmentalize the tunnel system by creating temporary barriers that can contain the propagation of flooding until a more permanent solution can be implemented. One way to create a temporary barrier is by the deployment of a large-scale inflatable structure, also known as an inflatable plug. In such an application, the inflatable structure is prepared for placement, either permanently or temporally, and maintained ready for deployment, inflation, and pressurization when needed. The internal plug pressure imparts a normal force against the tunnel wall surface with the friction between the plug and tunnel surfaces opposing axial movement of the plug. The sealing effectiveness depends on the ability of the inflatable structure to self-deploy and fit, without human intervention, to the intricacies of the perimeter of the conduit being sealed. Primary design constraints include having the plug stowed away from the dynamic envelope of the trains and being able to withhold the pressure of the flooding water. This work presents a compilation of the main aspects of the activities completed for the development of large-scale inflatable structures as part of the Resilient Tunnel Plug (RTP) Project. The main test results and lessons learned are presented to demonstrate the viability of implementing large-scale inflatable plugs for the containment of flooding in rail tunnels systems. Over 400 coupon and specimen tests, 200 reduced scale tests, and 100 full-scale tests were conducted to demonstrate the efficacy of the design of different prototypes over a 10-year research and development project. The culmination of the work was 12 large-scale flooding demonstrations where the inflatable tunnel plug was shown able to be deployed remotely and withstand a simulated flooding event.

42 ENGINEERING↗

DOE OSTI2020

Anomalies, a mod 2 index, and dynamics of 2d adjoint QCD

We show that 2 2 d adjoint QCD, an SU(N) S U ( N ) gauge theory with one massless adjoint Majorana fermion, has a variety of mixed ’t Hooft anomalies. The anomalies are derived using a recent mod 2 2 index theorem and its generalization that incorporates ’t Hooft flux. Anomaly matching and dynamical considerations are used to determine the ground-state structure of the theory. The anomalies, which are present for most values of N N , are matched by spontaneous chiral symmetry breaking. We find that massless 2 2 d adjoint QCD confines for N >2 N > 2 , except for test charges of N N -ality N/2 N / 2 , which are deconfined. In other words, \mathbb Z_N ℤ N center symmetry is unbroken for odd N N and spontaneously broken to \mathbb Z_{N/2} ℤ N / 2 for even N N . All of these results are confirmed by explicit calculations on small \mathbb{R}\times S^1 ℝ × S 1 . We also show that this non-supersymmetric theory exhibits exact Bose-Fermi degeneracies for all states, including the vacua, when N N is even. Furthermore, for most values of N N , 2 2 d massive adjoint QCD describes a non-trivial symmetry-protected topological (SPT) phase of matter, including certain cases where the number of interacting Majorana fermions is a multiple of 8 8 . As a result, it fits into the classification of (1+1) ( 1 + 1 ) d SPT phases of interacting Majorana fermions in an interesting way.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2019

Hydrogen bond dynamics and conformational flexibility in antipsychotics

Effective treatment of disorders of the central nervous system can often be achieved using bioactive molecules of similar moieties to those known to be tolerable. A better understanding of the solid-state characteristics of such molecules could thereby create new opportunities for research on pharmaceutical preparations and drug prescriptions, while information about their rich intramolecular dynamics may well add an important aspect in the field of in silico drug discovery. As such, we have investigated three different antipsychotic drugs: haloperidol (C 21 H 23 ClFNO 2 , HAL), aripiprazole (C 23 H 27 Cl 2 N 3 O 2 , APZ) and quetiapine hemifumarate (C 21 H 25 N 3 O 2 S·0.5C 4 H 4 O 4 , QTP) based on similarities either in their structures, hydrophobic and hydrophilic moieties, or in their modes of action, typical or atypical. Our aim was to test the structural and molecular stability of these three different antipsychotics. To this end, we compared the molecular vibrations observed by inelastic neutron spectroscopy of these systems with those from theoretical periodic calculations of the crystalline antipsychotics using the Vienna ab initio simulation package (VASP). While most of the observed features in the lattice region were reasonably well represented by the calculations, the overall spectra were relatively complex, and hence traditional assignment procedures for the approximately 600 normal modes in the unit cell were not possible. These results indicate that in the search for new drug candidates, not only analysis of the flexibility of the receptor, but also the dynamics of the active molecules play a role in improving the prediction of binding affinities.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Feasibility of an Accelerometer-Based Structural Health Monitoring System for the LANL Blast Tube

A modeling- and simulation-based study was conducted on the feasibility of implementing an accelerometer-based SHM system on the Los Alamos National Laboratory blast tube. A blast tube experiment was modeled using the Abaqus explicit finite element solver. A custom user subroutine was written to apply test-like pressure loading to the inside surface of the blast tube. The subroutine applies analytically defined pressure loads derived from tracer output taken from a Compressible Flow Computational Fluid Dynamics Solver model of the blast tube. Five unique versions of the model were created: an undamaged reference model at 65°F was used as the baseline and compared to equivalent models at 10°F and 100°F. These three models were compared to models with small damage at the reference temperature. The two types of damage considered were a radial (circumferential) crack in the main tube body and a longitudinal crack in the supports. Acceleration outputs were extracted from accelerometer bodies included in the model and were post processed using a variety of standard SHM techniques. Different potential features signaling failure were extracted and compared using statistical methods in the time and frequency domains. A method was identified that clearly shows that differences in structural response resulting from the modeled damage can be differentiated from the structural response resulting from changing environmental conditions. However, the amount of damage applied to create observable differences in the accelerometer data was so large that simpler methods of damage detection would be more cost effective in locating damage.

42 ENGINEERING↗

DOE OSTI2021

Pilot Testing of a Modular Oxygen Production System Using Oxygen Binding Adsorbents (Final Report)

In this project, RTI and Air Liquide have focused on the development of innovative oxygen separation materials and technologies based on reversibly binding of oxygen to enable smaller and cheaper air separations. In alignment with that object the team has had multiple achievements to advance the technology including: Synthesized and characterized novel M-CoSalen (RTIO2Sorb-1) material which showed a dynamic oxygen adsorption capacity in excess of 1wt%. Developed synthesis routes for RTIO2Sorb-1 with commercially relevant techniques and produced batches of 0.25kg and over 4 kg of total synthesis. Synthesized and characterized extrudate forms of the RTIO2Sorb-1 with relevant crush strength and maintained dynamic oxygen adsorption capacity in near 1wt%. Developed techniques for forming structured beds in fiber shapes with conventional materials. Developed a model for O 2 sorption processes to analyze various bed configurations and cycle parameters. Studied classic O 2 solid sorbents reported in the literature to learn oxygen binding mechanisms. Design a 10 kg/day O 2 VPSA pilot system with 2 or 4-bed operation. Completed a techno-economic analysis based on the experimental results and modeling. The overall objective of the project was to design, fabricate, and test a modular O 2 production system and perform a techno-economic analysis (TEA) after testing to determine the cost-benefit of the advanced modular air separation system. The goals of this technology development project were to achieve a bed-size factor (BSF) of less than 600 lb-adsorbent/TPD O 2 (ton/day O 2 ) (as compared with the state-of-the-art BSF of 850), and O 2 -purity greater than 95% at a cost that is projected to be equivalent or lower than the current state of the art (SOTA), commercially available large-scale cryogenic air separation systems. To achieve these goals and objective, the project team executed on (1) oxygen binding adsorbent optimization and scale up, (2) adsorbent material formation process studies to form the adsorbent material into structured beds for rapid pressure swing adsorption (PSA) cycles with low pressure drop, fast mass transfer, and low attrition, (3) cycle development studies to optimize the PSA process, and (4) develop simulation tools for rapid cycle modeling and numerical evaluation/optimization.

20 FOSSIL-FUELED POWER PLANTS↗

DOE OSTI2019

The combined force field-sampling problem in simulations of disordered amyloid-β peptides

Molecular dynamics simulations of intrinsically disordered proteins (IDPs) can provide high resolution structural ensembles if the force field is accurate enough and if the simulation sufficiently samples the conformational space of the IDP with the correct weighting of sub-populations. Here, we investigate the combined force field–sampling problem by testing a standard force field as well as newer fixed charge force fields, the latter specifically motivated for better description of unfolded states and IDPs, and comparing them with a standard temperature replica exchange (TREx) protocol and a non-equilibrium Temperature Cool Walking (TCW) sampling algorithm. The force field and sampling combinations are used to characterize the structural ensembles of the amyloid-beta peptides Aβ42 and Aβ43, which both should be random coils as shown recently by experimental nuclear magnetic resonance (NMR) and 2D Förster resonance energy transfer (FRET) experiments. The results illustrate the key importance of the sampling algorithm: while the standard force field using TREx is in poor agreement with the NMR J-coupling and nuclear Overhauser effect and 2D FRET data, when using the TCW method, the standard and optimized protein-water force field combinations are in very good agreement with the same experimental data since the TCW sampling method produces qualitatively different ensembles than TREx. Lastly, we also discuss the relative merit of the 2D FRET data when validating structural ensembles using the different force fields and sampling protocols investigated in this work for small IDPs such as the Aβ42 and Aβ43 peptides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Simultaneous bright- and dark-field X-ray microscopy at X-ray free electron lasers

Abstract The structures, strain fields, and defect distributions in solid materials underlie the mechanical and physical properties across numerous applications. Many modern microstructural microscopy tools characterize crystal grains, domains and defects required to map lattice distortions or deformation, but are limited to studies of the (near) surface. Generally speaking, such tools cannot probe the structural dynamics in a way that is representative of bulk behavior. Synchrotron X-ray diffraction based imaging has long mapped the deeply embedded structural elements, and with enhanced resolution, dark field X-ray microscopy (DFXM) can now map those features with the requisite nm-resolution. However, these techniques still suffer from the required integration times due to limitations from the source and optics. This work extends DFXM to X-ray free electron lasers, showing how the $$10^{12}$$ 10 12 photons per pulse available at these sources offer structural characterization down to 100 fs resolution (orders of magnitude faster than current synchrotron images). We introduce the XFEL DFXM setup with simultaneous bright field microscopy to probe density changes within the same volume. This work presents a comprehensive guide to the multi-modal ultrafast high-resolution X-ray microscope that we constructed and tested at two XFELs, and shows initial data demonstrating two timing strategies to study associated reversible or irreversible lattice dynamics.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c</em

Amide I difference spectroscopy is widely used to investigate protein function and structure changes. In this article, we show that the common approach of assigning features in amide I difference signals to distinct secondary structure elements in many cases may not be justified. Evidence comes from Fourier transform infrared (FTIR) and 2D-IR spectroelectrochemistry of the protein cytochrome c in the amide I range, in combination with computational spectroscopy based on molecular dynamics (MD) simulations. This combination reveals that each secondary structure unit, such as an alpha-helix or a beta-sheet, exhibits broad overlapping contributions, usually spanning a large part of the amide I region, which in the case of difference absorption experiments (such as in FTIR spectroelectrochemistry) may lead to intensity-compensating and even sign-changing contributions. We use cytochrome c as the test case, as this small electron-transferring redox-active protein contains different kinds of secondary structure units. Upon switching its redox-state, the protein exhibits a different charge distribution while largely retaining its structural scaffold. Our theoretical analysis suggests that the change in charge distribution contributes to the spectral changes and that structural changes are small. However, in order to confidently interpret FTIR amide I difference signals in cytochrome c and proteins in general, MD simulations in combination with additional experimental approaches such as isotope labeling, the insertion of infrared labels to selectively probe local structural elements will be required. In case these data are not available, a critical assessment of previous interpretations of protein amide I 1D- and 2D-IR difference spectroscopy data is warranted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Surfactant-Specific AI-Driven Molecular Design: Integrating Generative Models, Predictive Modeling, and Reinforcement Learning for Tailored Surfactant Synthesis

Molecular design is a critical aspect of various scientific and industrial fields, where the properties of molecules hold significant importance. In this study, a 3-fold methodology design is presented that leverages the power of generative artificial intelligence (AI), predictive modeling, and reinforcement learning to create tailored molecules with desired properties. This model synergistically combines deep learning techniques with Self-Referencing Embedded Strings (SELFIES) molecular representation to build a generative model that generates valid molecules and a graphical neural network model that accurately forecasts molecular properties. The Variational Autoencoder (VAE) coupled with reinforcement learning helps refine molecule generation based on targeted attributes. Data from an experimental study involving surfactants were used to test the framework. A validation of the structural integrity of the molecules generated was conducted, and Tanimoto similarities were used to quantify the similarity and diversity between the original and generated molecular structures. Also, saliency maps for the generated surfactants were produced to identify the features explaining the property values. Lastly, molecular dynamics simulations were used to validate the stability of the generated molecules. The results showed that the proposed framework can effectively produce valid molecules within the set property threshold value.

36 MATERIALS SCIENCE↗