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NASA NTRS1998

Pharmacy in Space: A Session on NASA Technologies

In 1993, Vice-president Gore was charged with creation of a correctional plan for the poor findings from an efficiency study of governmental agencies. That correctional analysis was then used to support efforts to balance the budget in ways anticipated to improve the value returned per tax payer dollar spent. The final result was a broad initiative collectively termed "reinventing the government", which included major restructuring within NASA as well, termed "reinventing NASA This included substantial elimination of middle management and downsizing such that about 2 million government workers employed in 1992 has shrunk now to about 1.2 million government workers who are employed in ways that at least somewhat decrease bureaucratic and programmatic inefficiencies. Today, "reinvented NASA" has an awareness of contractual commitment to the public. NASA now operates within a so-called "strategic plan" that requires awareness and response to domestic needs. This is important to this audience because it means that NASA is committed to exploring interactions that you may wish to initiate. That is, you are urged to explore with NASA on topics of educational support, collaborative research, or commercial partnerships in drug development and application, as the pertinent examples here, in ways that can include involvement of central NASA resources and missions.

Richmond, Robert C.↗

NASA NTRS1999

Ambient Light Intensity, Actigraphy, Sleep and Respiration, Circadian Temperature and Melatonin Rhythms and Daytime Performance of Crew Members During Space Flight on STS-90 and STS-95 Missions

Sleep disruption and associated waking sleepiness and fatigue are common during space flight. A survey of 58 crew members from nine space shuttle missions revealed that most suffered from sleep disruption, and reportedly slept an average of only 6.1 hours per day of flight as compared to an average of 7.9 hours per day on the ground. Nineteen percent of crewmembers on single shift missions and 50 percent of the crewmembers in dual shift operations reported sleeping pill usage (benzodiazepines) during their missions. Benzodiazepines are effective as hypnotics, however, not without adverse side effects including carryover sedation and performance impairment, anterograde amnesia, and alterations in sleep EEG. Our preliminary ground-based data suggest that pre-sleep administration of 0.3 mg of the pineal hormone melatonin may have the acute hypnotic properties needed for treating the sleep disruption of space flight without producing the adverse side effects associated with benzodiazepines. We hypothesize that pre-sleep administration of melatonin will result in decreased sleep latency, reduced nocturnal sleep disruption, improved sleep efficiency, and enhanced next-day alertness and cognitive performance both in ground-based simulations and during the space shuttle missions. Specifically, we have carried out experiments in which: (1) ambient light intensity aboard the space shuttle is assessed during flight; (2) the impact of space flight on sleep (assessed polysomnographically and actigraphically), respiration during sleep, circadian temperature and melatonin rhythms, waking neurobehavioral alertness and performance is assessed in crew members of the Neurolab and STS-95 missions; (3) the effectiveness of melatonin as a hypnotic is assessed independently of its effects on the phase of the endogenous circadian pacemaker in ground-based studies, using a powerful experimental model of the dyssomnia of space flight; (4) the effectiveness of melatonin as a hypnotic is assessed during the STS-90 (Neurolab) and STS-95 missions in a double-blind placebo-controlled trial. In both flight-based experiments, the effects of melatonin on sleep stages and spectral composition of the EEG during sleep will be determined as well as its effects on daytime alertness and performance; (5) the impact of space flight on sleep and waking neurobehavioral alertness and performance in 30-45-year-old astronauts is compared with its impact in a 77-year-old astronaut. This case study is the first to assess the effects of space flight on an older individual. Because the investigators are still blind to the treatment in this double-blind, placebo-controlled trial, preliminary results will be presented independent of the drug condition.

Czeisler, Charles A.↗

NASA NTRS1999

Non-Invasive Assessment of Susceptibility to Ventricular Arrhythmias During Simulated Microgravity

The Cardiovascular Alterations Team is currently conducting studies to determine what alterations in hemodynamic regulation result from sixteen days of simulated microgravity exposure in normal human subjects. In this project we make additional measurements on these same study subjects in order to determine whether there is an increase in susceptibility to ventricular arrhythmias resulting from simulated microgravity exposure. Numerous anecdotal and documented reports from the past 30 years suggest that the incidence of ventricular arrhythmias among astronauts is increased during space flight. For example, documented runs of ventricular tachycardia have been recorded from crew members of Skylab and Mir, there was much attention given by the lay press to Mir Commander Vasily Tslbliyev's complaints of heart rhythm irregularities in July of 1997, and cardiovascular mechanisms may have been causal in the recent death of an experimental primate shortly after return from space. In 1986, a Mir cosmonaut, Alexander Laveikin, was brought home and replaced with an alternate cosmonaut as a result of cardiac dysrhythmias that began during extravehicular activity. Furthermore, at a joint NASA/NSBRI workshop held in January 1998, cardiac arrhythmias were identified as the highest priority cardiovascular risk to a human Mars mission. Despite the evidence for the risk of a potentially lethal arrhythmia resulting from microgravity exposure, the effects of space flight and the associated physiologic stresses on cardiac conduction processes are not known, and an increase in cardiac susceptibility to arrhythmias has never been quantified. In this project, we are determining whether simulated space flight increases the risk of developing life-threatening heart rhythm disturbances such as sustained ventricular tachycardia (defined as ventricular tachycardia lasting at least 30 seconds or resulting in hemodynamic collapse) and ventricular fibrillation. We are obtaining measures of cardiac susceptibility to ventricular arrhythmias in subjects exposed to simulated space flight in the Human Studies Core protocol being conducted by the Cardiovascular Alterations Team, which involves sixteen days .of bed rest. In particular, we are applying a powerful new non-invasive technology, developed in Professor Cohen's laboratory at MIT for the quantitative assessment of the risk of life-threatening ventricular arrhythmias. This technology involves the measurement of microvolt levels of T wave alternans (TWA) during exercise stress, and was recently granted approval by the Food and Drug Administration to be used for the clinical evaluation of patients suspected to be at risk of ventricular arrhythmias. In addition, we are obtaining 24 hour Holter monitoring (to detect non-sustained ventricular tachycardia and to assess heart rate variability). We are also conducting protocols to obtain these same measures on a monthly basis for up to four months in subjects in the Bone Demineralization/calcium Metaboloism Team's long term bed rest study.

Cohen, Richard J.↗

NASA NTRS1999

Chemoprevention of Radiation Induced Rat Mammary Neoplasms

Radiations encountered in space include protons and heavy ions such as iron as well as their secondaries. The relative biological effect (RBE) of these ions is not known, particularly at the doses and dose-rates expected for planetary missions. Neutrons, are not particularly relevant to space travel, but have been found experimentally to have an increase in their RBE with decreasing dose. If a similar trend of increasing RBE with decreasing dose is present for heavy ions and protons during irradiation in space, the small doses received during space travel could potentially have substantial carcinogenic risk. Clearly more investigation of the effects of heavy ions and protons is needed before accurate risk assessment for prolonged travel in space can be done. One means to mitigate the increased risk of cancer due to radiation exposure in space is by developing effective countermeasures that can reduce the incidence of tumor development. Tamoxifen has recently been shown to be an effective chemopreventive agent in both animal models and humans for the prevention of mammary tumors. Tamoxifen is a unique drug, with a highly specific mechanism of action affecting a specific radiation-sensitive population of epithelial cells in the mammary gland. In human studies, the annual incidence of a primary tumor in the contralateral breast of women with previous breast cancer is about 8 per 1000, making them an exceedingly high-risk group for the development of breast cancer. In this high risk group, treated with tamoxifen, daily, for 2 years, the incidence of a new primary tumor in the contralateral breast was approximately one third of that noted in the non-tamoxifen treatment group. Tamoxifen antagonizes the action of estrogen by competing for the nuclear receptor complex thereby altering the association of the receptor complex and nuclear binding sites. Its effects in reducing the development of breast cancer could be accomplished by controlling clinically undetectable microcancers, arresting preneoplastic lesions, or correcting abnormal environments which predispose to high risk of malignant transformation.

Huso, David L.↗

NASA NTRS1995

Exercise and Human Immunodeficiency Virus (HIV-1) Infection

The human immune system is highly efficient and remarkably protective when functioning properly. Similar to other physiological systems, it functions best when the body is maintained with a balanced diet, sufficient rest and a moderately stress-free lifestyle. It can be disrupted by inappropriate drug use and extreme emotion or exertion. The functioning of normal or compromised immune systems can be enhanced by properly prescribed moderate exercise conditioning regimens in healthy people, and in some human immunodeficiency virus (HIV-1)-infected patients but not in others who unable to complete an interval training program. Regular exercise conditioning in healthy people reduces cardiovascular risk factors, increases stamina, facilitates bodyweight control, and reduces stress by engendering positive feelings of well-being. Certain types of cancer may also be suppressed by appropriate exercise conditioning. Various exercise regimens are being evaluated as adjunct treatments for medicated patients with the HIV-1 syndrome. Limited anecdotal evidence from patients suggests that moderate exercise conditioning is per se responsible for their survival well beyond expectancy. HIV-1-infected patients respond positively, both physiologically and psychologically, to moderate exercise conditioning. However, the effectiveness of any exercise treatment programme depends on its mode, frequency, intensity and duration when prescribed o complement the pathological condition of the patient. The effectiveness of exercise conditioning regimens in patients with HIV-1 infection is reviewed in this article. In addition, we discuss mechanisms and pathways, involving the interplay of psychological and physiological factors, through which the suppressed immune system can be enhanced. The immune modulators discussed are endogenous opioids, cytokines, neurotransmitters and other hormones. Exercise conditioning treatment appears to be more effective when combined with other stress management procedures.

Lawless, DeSales↗

NASA NTRS2000

Growth of Carbon Nanostructure Materials Using Laser Vaporization

Since the potential applications of carbon nanotubes (CNT) was discovered in many fields, such as non-structure electronics, lightweight composite structure, and drug delivery, CNT has been grown by many techniques in which high yield single wall CNT has been produced by physical processes including arc vaporization and laser vaporization. In this presentation, the growth mechanism of the carbon nanostructure materials by laser vaporization is to be discussed. Carbon nanoparticles and nanotubes have been synthesized using pulsed laser vaporization on Si substrates in various temperatures and pressures. Two kinds of targets were used to grow the nanostructure materials. One was a pure graphite target and the other one contained Ni and Co catalysts. The growth temperatures were 600-1000 C and the pressures varied from several torr to 500 torr. Carbon nanoparticles were observed when a graphite target was used, although catalysts were deposited on substrates before growing carbon films. When the target contains catalysts, carbon nanotubes (CNT) are obtained. The CNT were characterized by scanning electron microscopy, x-ray diffraction, optical absorption and transmission, and Raman spectroscopy. The temperature-and pressure-dependencies of carbon nanotubes' growth rate and size were investigated.

Zhu, Shen↗

NASA NTRS2000

Fluid Physics and Macromolecular Crystal Growth in Microgravity

Pusey, M.↗

NASA NTRS2000

Fluid Physics and Macromolecular Crystal Growth in Microgravity

The first protein crystallization experiment in microgravity was launched in April, 1981 and used Germany's Technologische Experimente unter Schwerelosigkeit (TEXUS 3) sounding rocket. The protein P-galactosidase (molecular weight 465Kda) was chosen as the sample with a liquid-liquid diffusion growth method. A sliding device brought the protein, buffer and salt solution into contact when microgravity was reached. The sounding rocket gave six minutes of microgravity time with a cine camera and schlieren optics used to monitor the experiment, a single growth cell. In microgravity a strictly laminar diffusion process was observed in contrast to the turbulent convection seen on the ground. Several single crystals, approx 100micron in length, were formed in the flight which were of inferior but of comparable visual quality to those grown on the ground over several days. A second experiment using the same protocol but with solutions cooled to -8C (kept liquid with glycerol antifreeze) again showed laminar diffusion. The science of macromolecular structural crystallography involves crystallization of the macromolecule followed by use of the crystal for X-ray diffraction experiments to determine the three dimensional structure of the macromolecule. Neutron protein crystallography is employed for elucidation of H/D exchange and for improved definition of the bound solvent (D20). The structural information enables an understanding of how the molecule functions with important potential for rational drug design, improved efficiency of industrial enzymes and agricultural chemical development. The removal of turbulent convection and sedimentation in microgravity, and the assumption that higher quality crystals will be produced, has given rise to the growing number of crystallization experiments now flown. Many experiments can be flown in a small volume with simple, largely automated, equipment - an ideal combination for a microgravity experiment. The term "protein crystal growth" is often historically used to describe these microgravity experiments. This is somewhat inaccurate as the field involves the study of many varied biological molecules including viruses, proteins, DNA, RNA and complexes of those structures. For this reason we use the term macromolecular crystal growth. In this chapter we review a series of diagnostic microgravity crystal growth experiments carried out principally using the European Space Agency (ESA) Advanced Protein Crystallization Facility (APCF). We also review related research, both experimental and theoretical, on the aspects of microgravity fluid physics that affect microgravity protein crystal growth. Our experiments have revealed some surprises that were not initially expected. We discuss them here in the context of practical lessons learnt and how to maximize the limited microgravity opportunities available.

Helliwell, John R.↗

NASA NTRS1997

Free Radicals Generated by Ionizing Radiation Signal Nuclear Translocation of p53

The p53 tumor suppressor is a transcription factor that regulates several pathways, which function collectively to maintain the integrity of the genome. Nuclear localization is critical for wild-type function. However, the signals that regulate subcellular localization of p53 have not been identified. Here, we examine the effect of ionizing radiation on the subcellular localization of p53 in two cell lines in which p63 is normally sequestered in the cytoplasm and found that ionizing radiation caused a biphasic translocation response. p53 entered the nucleus 1-2 hours postirradiation (early response), subsequently emerged from the nucleus, and then again entered the nucleus 12-24 hours after the cells had been irradiated (delayed response). These changes in subcellular localization could be completely blocked by the free radical scavenger, WR1065. By comparison, two DNA-damaging agents that do not generate free radicals, mitomycin C and doxorubicin, caused translocation only after 12-24 h of exposure to the drugs, and this effect could not be inhibited by WR1065. Hence, although all three DNA-damaging agents induced relocalization of p53 to the nucleus, only the translocation caused by radiation was sensitive to free radical scavenging. We suggest that the free radicals generated by ionizing radiation can signal p53 translocation to the nucleus.

Martinez, J. D.↗

NASA NTRS2000

Biotechnology Facility: An ISS Microgravity Research Facility

The International Space Station (ISS) will support several facilities dedicated to scientific research. One such facility, the Biotechnology Facility (BTF), is sponsored by the Microgravity Sciences and Applications Division (MSAD) and developed at NASA's Johnson Space Center. The BTF is scheduled for delivery to the ISS via Space Shuttle in April 2005. The purpose of the BTF is to provide: (1) the support structure and integration capabilities for the individual modules in which biotechnology experiments will be performed, (2) the capability for human-tended, repetitive, long-duration biotechnology experiments, and (3) opportunities to perform repetitive experiments in a short period by allowing continuous access to microgravity. The MSAD has identified cell culture and tissue engineering, protein crystal growth, and fundamentals of biotechnology as areas that contain promising opportunities for significant advancements through low-gravity experiments. The focus of this coordinated ground- and space-based research program is the use of the low-gravity environment of space to conduct fundamental investigations leading to major advances in the understanding of basic and applied biotechnology. Results from planned investigations can be used in applications ranging from rational drug design and testing, cancer diagnosis and treatments and tissue engineering leading to replacement tissues.

Gonda, Steve R.↗

NASA NTRS2000

JavaGenes and Condor: Cycle-Scavenging Genetic Algorithms

A genetic algorithm code, JavaGenes, was written in Java and used to evolve pharmaceutical drug molecules and digital circuits. JavaGenes was run under the Condor cycle-scavenging batch system managing 100-170 desktop SGI workstations. Genetic algorithms mimic biological evolution by evolving solutions to problems using crossover and mutation. While most genetic algorithms evolve strings or trees, JavaGenes evolves graphs representing (currently) molecules and circuits. Java was chosen as the implementation language because the genetic algorithm requires random splitting and recombining of graphs, a complex data structure manipulation with ample opportunities for memory leaks, loose pointers, out-of-bound indices, and other hard to find bugs. Java garbage-collection memory management, lack of pointer arithmetic, and array-bounds index checking prevents these bugs from occurring, substantially reducing development time. While a run-time performance penalty must be paid, the only unacceptable performance we encountered was using standard Java serialization to checkpoint and restart the code. This was fixed by a two-day implementation of custom checkpointing. JavaGenes is minimally integrated with Condor; in other words, JavaGenes must do its own checkpointing and I/O redirection. A prototype Java-aware version of Condor was developed using standard Java serialization for checkpointing. For the prototype to be useful, standard Java serialization must be significantly optimized. JavaGenes is approximately 8700 lines of code and a few thousand JavaGenes jobs have been run. Most jobs ran for a few days. Results include proof that genetic algorithms can evolve directed and undirected graphs, development of a novel crossover operator for graphs, a paper in the journal Nanotechnology, and another paper in preparation.

Globus, Al↗

NASA NTRS1999

Induction of Three-Dimensional Growth of Human Liver Cells in Simulated Microgravity

We previously reported that a NASA-developed bioreactor that simulates microgravity environment and creates the unique environment of low shear force and high-mass transfer is conducive for maintaining long term 3-D cell cultures of functional hepatocytes (60 days). However, significant further expansion of liver mass, or the remodeling of liver in vitro was jeopardized by the appearance of apoptotic zones in the center of large cell aggregates. To optimize oxygenation and nutritional uptake within growing cellular aggregates we cultured primary human liver cells (HLC) in a bioreactor in the presence or absence of microcarriers and biodegradable scaffolds. Also, to promote angiogenesis, HLC were cultured with or without microvascular endothelial cells. HLC were harvested from human livers by collagenase perfusion. While microcarriers did not affect cell growth, HLC cultured with biodegradable scaffolds made from polyglycolic acid (PGA) formed aggregates up to 3 cm in length. Culturing cells with PGA scaffolds increased the efficiency of cell self-assembly and the formation of larger cell aggregates. Based on histological evaluation it appears that the degree of apoptotic cells was diminished as compared to cultures without scaffolds. Histology of HLC with PGA-scaffolds revealed cell distribution between the fibers of the scaffolds, and cell-cell and cell-fiber interactions. Analyses of HLC spheroids revealed tissue-like structures comprised of hepatocytes, biliary epithelial cells and/or progenitor liver cells that were arranged as bile duct-like structures along nascent vascular sprouts. Electron microscopy revealed groups of cohesive hepatocytes and bile canaliculi with multiple microvilli and tight cellular junctions. Hepatocytes were further organized into tight clusters surrounded by complex stromal structures and reticulin fibers. Also, we observed higher levels of albumin mRNA expression when hepatocytes were co-cultured with endothelial cells. To evaluate viability and microsomal deethylation activity of hepatocytes we assessed the metabolism of midazolam by gas chromatography. Samples that were collected from HLC cultured in the bioreactor contained higher levels of midazolam metabolites (1-OH-midazolam and 4-OH-midazolam) than samples collected from conventional cultures. In summary, we have shown that co-culture of HLC with endothelial cells and/or culturing in the presence of PGA scaffolds provides additional advantages in maintaining functional activity of 3-D hepatocyte cultures that resemble liver tissue. This cell culture system may facilitate studies of liver regeneration and cell-to-cell interactions that occur in vivo and suggest the feasibility of using this approach for pre-clinical metabolic screening of novel drug candidates.

Pellis, Neal R.↗

NASA NTRS2000

A New Clinical Instrument for The Early Detection of Cataract Using Dynamic Light Scattering and Corneal Topography

A growing cataract can be detected at the molecular level using the technique of dynamic light scattering (DLS). However, the success of this method in clinical use depends upon the precise control of the scattering volume inside a patient's eye and especially during patient's repeat visits. This is important because the scattering volume (cross-over region between the scattered fight and incident light) inside the eye in a high-quality DLS set-up is very small (few microns in dimension). This precise control holds the key for success in the longitudinal studies of cataract and during anti-cataract drug screening. We have circumvented these problems by fabricating a new DLS fiber optic probe with a working distance of 40 mm and by mounting it inside a cone of a corneal analyzer. This analyzer is frequently used in mapping the corneal topography during PRK (photorefractive keratectomy) and LASIK (laser in situ keratomileusis) procedures in shaping of the cornea to correct myopia. This new instrument and some preliminary clinical tests on one of us (RRA) showing the data reproducibility are described.

Ansari, Rafat R.↗

NASA NTRS2000

Microencapsulation and Electrostatic Processing Method

Methods are provided for forming spherical multilamellar microcapsules having alternating hydrophilic and hydrophobic liquid layers, surrounded by flexible, semi-permeable hydrophobic or hydrophilic outer membranes which can be tailored specifically to control the diffusion rate. The methods of the invention rely on low shear mixing and liquid-liquid diffusion process and are particularly well suited for forming microcapsules containing both hydrophilic and hydrophobic drugs. These methods can be carried out in the absence of gravity and do not rely on density-driven phase separation, mechanical mixing or solvent evaporation phases. The methods include the process of forming, washing and filtering microcapsules. In addition, the methods contemplate coating microcapsules with ancillary coatings using an electrostatic field and free fluid electrophoresis of the microcapsules. The microcapsules produced by such methods are particularly useful in the delivery of pharmaceutical compositions.

Morrison, Dennis R.↗

NASA NTRS2000

Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm

One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous mixing. A similar difficulty may be encountered in any method relying on global modifications of phase space.

Darve, Eric↗

NASA NTRS2000

Fluid Physics and Macromolecular Crystal Growth in Microgravity

The molecular structure of biological macromolecules is important in understanding how these molecules work and has direct application to rational drug design for new medicines and for the improvement and development of industrial enzymes. In order to obtain the molecular structure, large, well formed, single macromolecule crystals are required. The growth of macromolecule crystals is a difficult task and is often hampered on the ground by fluid flows that result from the interaction of gravity with the crystal growth process. One such effect is the bulk movement of the crystal through the fluid due to sedimentation. A second is buoyancy driven convection close to the crystal surface. On the ground the crystallization process itself induces both of these flows. Buoyancy driven convection results from density differences between the bulk solution and fluid close to the crystal surface which has been depleted of macromolecules due to crystal growth. Schlieren photograph of a growing lysozyme crystal illustrating a 'growth plume' resulting from buoyancy driven convection. Both sedimentation and buoyancy driven convection have a negative effect on crystal growth and microgravity is seen as a way to both greatly reduce sedimentation and provide greater stability for 'depletion zones' around growing crystals. Some current crystal growth hardware however such as those based on a vapor diffusion techniques, may also be introducing unwanted Marangoni convection which becomes more pronounced in microgravity. Negative effects of g-jitter on crystal growth have also been observed. To study the magnitude of fluid flows around growing crystals we have attached a number of different fluorescent probes to lysozyme molecules. At low concentrations, less than 40% of the total protein, the probes do not appear to effect the crystal growth process. By using these probes we expect to determine not only the effect of induced flows due to crystal growth hardware design but also hope to optimize crystallization hardware so that destructive flows are minimized both on the ground and in microgravity.

Pusey, M.↗

NASA NTRS2001

Proton Pumps: Mechanism of Action and Applications

Recent progress in understanding molecular structures and mechanisms of action of proton pumps has paved the way to their novel applications in biotechnology. Proton pumps, in particular bacteriorhodopsin and ATP synthases, are capable of continuous, renewable conversion of light to chemical, mechanical or electrical energy, which can be used in macro- or nano-scale devices. The capability of protein systems incorporated into liposomes to generate ATP, which can be further used to drive chemical reactions, and to act as molecular motors has been already demonstrated. Other possible applications of such biochemical devices include targeted drug delivery and biocatalytic re actors. All these devices might prove superior to their inorganic alternatives.

Lanyi, Janos K.↗

NASA NTRS2001

Better, Cheaper, Faster Molecular Dynamics

Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.

Pohorille, Andrew↗