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At least 1,369 records · Page 76

The effect of protein mutations on drug binding suggests ensuing personalised drug selection

The advent of personalised medicine promises a deeper understanding of mechanisms and therefore therapies. However, the connection between genomic sequences and clinical treatments is often unclear. We studied 50 breast cancer patients belonging to a population-cohort in the state of Qatar. From Sanger sequencing, we identified several new deleterious mutations in the estrogen receptor 1 gene (ESR1). The effect of these mutations on drug treatment in the protein target encoded by ESR1, namely the estrogen receptor, was achieved via rapid and accurate protein–ligand binding affinity interaction studies which were performed for the selected drugs and the natural ligand estrogen. Four nonsynonymous mutations in the ligand-binding domain were subjected to molecular dynamics simulation using absolute and relative binding free energy methods, leading to the ranking of the efficacy of six selected drugs for patients with the mutations. Our study shows that a personalised clinical decision system can be created by integrating an individual patient’s genomic data at the molecular level within a computational pipeline which ranks the efficacy of binding of particular drugs to variant proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Biphasic solvents for post-combustion CO 2 capture from natural gas flue Gas

Fossil fuel fired power plants are generally expected to remain one of the most significant global sources of electricity for decades to come. Consequently, carbon management technologies are needed to reduce or eliminate ongoing emissions from these sources. Amongst the many techniques for carbon capture, aqueous amine-based absorbents (monoethanolamine, MEA, in particular) are, presently, considered the leading technology for post-combustion CO 2 point-source capture. These technologies are nevertheless limited by their high capital and regeneration energy costs. Biphasic solvents have been identified as an attractive alternative to traditional MEA based absorbents due to their potential energy savings. Thus far, however, the research on biphasic solvents has largely focused on their performance in coal flue gas while more dilute natural gas flue gas applications have received relatively little attention. Here, this work examines the performances of two novel biphasic solvent blends, diethylenetriamine (DETA) and triethylenetetramine (TETA), in CO 2 capture from a natural gas flue gas simulant. Across several regeneration tests, both solvents achieved considerable energy savings over the benchmark MEA solution. Specifically, the energy consumption per mol CO 2 recovered for the DETA-based and TETA-based solvents was 46 % and 35 % less than that of the benchmark MEA solution, respectively. Molecular dynamics simulations were also performed to gain a deeper understanding of the phase separation phenomena that occur as a consequence of CO 2 absorption. These simulations indicated that phase change was driven by the strong interaction between the absorption products and water, while the degree of separation depended on the CO 2 loading.

Biphasic solvents↗

Nonlinear Shear Rheology of Entangled Polymer Rings

Steady-state shear viscosity η($\bar{γ}$) of unconcatenated ring polymer melts as a function of the shear rate $\bar{γ}$ is studied by a combination of experiments, simulations, and theory. Experiments using polystyrenes with Z ≈ 5 and Z ≈ 11 entanglements indicate weaker shear thinning for rings compared to linear polymers exhibiting power law scaling of shear viscosity η ~ $\bar{γ}$ –0.56 ± 0.02 , independent of chain length, for Weissenberg numbers up to about 10 2 . Nonequilibrium molecular dynamics simulations using the bead-spring model reveal a similar behavior with η ~ $\bar{γ}$ -0.57 ± 0.08 for 4 ≤ Z ≤ 57. Viscosity decreases with chain length for high $\bar{γ}$. In our experiments, we see the onset of this regime, and in simulations, which we extended to Wi ~ 10 4 , the nonuniversality is fully developed. In addition to a naive scaling theory yielding for the universal regime η ~ $\bar{γ}$ –0.57 , we developed a novel shear slit model explaining many details of observed conformations and dynamics as well as the chain length-dependent behavior of viscosity at large $\bar{γ}$. The signature feature of the model is the presence of two distinct length scales: the size of tension blobs and much larger thickness of a shear slit in which rings are self-consistently confined in the velocity gradient direction and which is dictated by the size of a chain section with relaxation time 1/$\bar{γ}$. These two length scales control the two normal stress differences. In this model, the chain length-dependent onset of nonuniversal behavior is set by tension blobs becoming as small as about one Kuhn segment. This model explains the approximate applicability of the Cox–Merz rule for ring polymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomistic Materials Modeling of High-Pressure Hydrogen Interactions in Ethylene Propylene Diene Monomer (EPDM) Rubber

Elastomeric rubbers serve a vital role as sealing materials in the hydrogen storage and transport infrastructure. With applications including O-rings and hose-liners, these components are exposed to pressurized hydrogen at a range of temperatures, cycling rates, and pressure extremes. Cyclic (de)pressurization is known to degrade these materials through the process of cavitation. This readily visible failure mode occurs as a fracture or rupture of the material and is due to the oversaturated gas localizing to form gas bubbles. Computational modeling in the Hydrogen Materials Compatibility Program (H-Mat), co-led by Sandia National Laboratories and Pacific Northwest National Laboratory, employs multi-scale simulation efforts to build a predictive understanding of hydrogen-induced damage in materials. Modeling efforts within the project aim to provide insight into how to formulate materials that are less sensitive to high-pressure hydrogen-induced failure. In this document, we summarize results from atomistic molecular dynamics simulations, which make predictive assessments of the effects of compositional variations in the commonly used elastomer, ethylene propylene diene monomer (EPDM).

08 HYDROGEN↗

Computer Simulation Studies of Ion Channel Gating: Characteristics of the M2 Channel of Influenza-A Virus in a Phospholipid Bilayer

The 25 amino acids long, transmembrane fragment of the Influenza virus M2 protein forms a homotetrameric channel that transports protons across lipid bilayers. It has been postulated that high efficiency and selectivity of this process is due to gating by four histidine residues that occlude the channel lumen in the closed state. Two mechanisms of gating have been postulated. In one mechanism, the proton is "shuttled" through the gate by attaching to the delta nitrogen atom on the extracellular side of the imidazole ring, followed by the release of the proton attached to the epsilon nitrogen atom on the opposite side. In the second mechanism, the four histidines move away from each other due to electrostatic repulsion upon protonation, thus opening the gate sufficiently that a wire of water molecules can penetrate the gate. Then, protons are transported by "hopping" along the wire. In this paper, both mechanisms are evaluated in a series of molecular dynamics simulations by investigating stability of different protonation states of the channel that are involved in these mechanisms. For the shuttle mechanism, these are states with all epsilon protonated histidines, one biprotonated residue or one histidine protonated in the delta position. For the gate opening mechanism, this is the state in which all four histidines are biprotonated. In addition, a state with two biprotonated histidines is considered. For each system, composed of the protein channel embedded in phospholipid bilayer located between two water lamellae, a molecular dynamics trajectory of approximately 1.3 ns (after equilibration) was obtained. It is found that the states involved in the shuttle mechanism are stable during the simulations. Furthermore, the orientations and dynamics of water molecules near the gate are conducive to proton transfers involved in the shuttle. In contract, the fully biprotonated state, implicated in the gate opening mechanism, is not stable and the channel looses its structural integrity. If only two histidines are biprotonated the channel deforms but remains intact with the gate mostly closed. In summary, the results of this study lend support to the shuttle mechanism but not to the gate opening mechanism of proton gating in M2.

Schweighofer, Karl J.↗

Scanning the RBD-ACE2 molecular interactions in Omicron variant

The emergence of new SARS-CoV-2 variants poses a threat to the human population where it is difficult to assess the severity of a particular variant of the virus. Spike protein and specifically its receptor binding domain (RBD) which makes direct interaction with the ACE2 receptor of the human has shown prominent amino acid substitutions in most of the Variants of Concern. Here, in this work, by using all-atom molecular dynamics simulations we compare the interaction of Wild-type RBD/ACE2 receptor complex with that of the latest Omicron variant of the virus. We observed a very interesting diversification of the charge, dynamics and energetics of the protein complex formed upon mutations. These results would help us in understanding the molecular basis of binding of the Omicron variant with that of SARS-CoV-2 Wild-type.

60 APPLIED LIFE SCIENCES↗

Ab Initio Simulations of Phase Stability and Martensitic Transitions in NiTi

For NiTi based alloys, the shape memory effect is governed by a transition from a low-temperature martensite phase to a high-temperature austenite phase. Despite considerable experimental and computational work, basic questions regarding the stability of the phases and the martensitic phase transition remain unclear even for the simple case of binary, equiatomic NiTi. We perform ab initio molecular dynamics simulations to describe the temperature-dependent behavior of NiTi and resolve several of these outstanding issues. Structural correlation functions and finite temperature phonon spectra are evaluated to determine phase stability. We show that finite temperature, entropic effects stabilize the experimentally observed martensite (B19') and austenite (B2) phases while destabilizing the theoretically predicted (B33) phase. Free energy computations based on ab initio thermodynamic integration confirm these results and permit estimates of the transition temperature between the phases. In addition to the martensitic phase transition, we predict a new transition between the B33 and B19' phases. The role of defects in suppressing phase transformation temperatures is discussed.

Simulations↗

Simulation of Peptides at Aqueous Interfaces

Behavior of peptides at water-membrane interfaces is of great interest in studies on cellular transport and signaling, membrane fusion, and the action of toxins and antibiotics. Many peptides, which exist in water only as random coils, can form sequence-dependent, ordered structures at aqueous interfaces, incorporate into membranes and self-assembly into functional units, such as simple ion channels. Multi -nanosecond molecular dynamics simulations have been carried out to study the mechanism and energetics of interfacial folding of both non-polar and amphiphilic peptides, their insertion into membranes and association into higher-order structures. The simulations indicate that peptides fold non-sequentially, often through a series of amphiphilic intermediates. They further incorporate into the membrane in a preferred direction as folded monomers, and only then aggregate into dimers and, possibly, further into "dimers of dimers".

Pohorille, Andrew↗

Toward a First-Principles Framework for Predicting Collective Properties of Electrolytes

Conspectus Given the universal importance of electrolyte solutions, it is natural to expect that we have a nearly complete understanding of the fundamental properties of these solutions (e.g., the chemical potential) and that we can therefore explain, predict, and control the phenomena occurring in them. In fact, reality falls short of these expectations. But, recent advances in the simulation and modeling of electrolyte solutions indicate that it should soon be possible to make progress toward these goals. In this Account, we will discuss the use of first-principles interaction potentials based in quantum mechanics (QM) to enhance our understanding of electrolyte solutions. Specifically, we will focus on the use of quantum density functional theory (DFT) combined with molecular dynamics simulation (DFT-MD) as the foundation for our approach. The overarching concept is to understand and accurately reproduce the balance between local or short-ranged (SR) structural details and long-range (LR) correlations, allowing the prediction of the thermodynamics of both single ions in solution as well as the collective interactions characterized by activity/osmotic coefficients. In doing so, relevant collective motions and driving forces characterized by chemical potentials can be determined. Here, in this Account, we will make the case that understanding electrolyte solutions requires a faithful QM representation of the SR nature of the ion–ion, ion–water, and water–water interactions. However, the number of molecules that is required for collective behavior makes the direct application of high-level QM methods that contain the best SR physics untenable, making methods that balance accuracy and efficiency a practical goal. Alternatives such as continuum solvent models (CSMs) and empirically based classical molecular dynamics have been extensively employed to resolve this problem but without yet overcoming the fundamental issue of SR accuracy. We will demonstrate that accurately describing the SR interaction is imperative for predicting both intrinsic properties, namely, at infinite dilution, and collective properties of electrolyte solutions. DFT has played an important role in our understanding of condensed phase systems, e.g., bulk liquid water, the air–water interface, ions in bulk, and at the air–water interface. This approach holds huge promise to provide benchmark calculations of electrolyte solution properties that will allow for the development and improvement of more efficient methods, as well as an enhanced understanding of fundamental phenomena. However, the standard protocol using the generalized gradient approximation with van der Waals (vdW) correction requires improvement in order to achieve a high level of quantitative accuracy. Simply simulating with higher level DFT functionals may not be the best route considering the significant computational cost. Alternative methods of incorporating information from higher levels of QM should be explored; e.g., using force matching techniques on small clusters, where high level benchmark calculations are possible, to develop ideal correction terms to the DFT functional is a promising possibility. We argue that DFT with statistical mechanics is becoming an increasingly useful framework enabling the prediction of collective electrolyte properties.

Duignan, Timothy T.↗

Unraveling disadhesion mechanism of epoxy/CSH interface under aggressive conditions

Almost all FRP-reinforced concrete exposed to the marine environment are susceptible to durability deficiencies due to failure of the FRP/epoxy/concrete interface, especially the vulnerable epoxy/concrete interface, which is frequently attacked by water and ions. Herein, molecular dynamics simulations of epoxy/CSH interface under different environmental exposures are utilized to specifically elucidate the degradation principles of water and ions on the bonding properties and mechanical responses of the epoxy/concrete interface. The environmental sequences associated with the interfacial bonding degradation are arranged as Na{sub 2}SO{sub 4} + NaCl>NaCl>Na{sub 2}SO{sub 4} > Water>Dry. Remarkably, water molecules weaken the interaction between the epoxy and CSH by robbing interfacial H- and Ca-O bonds, thereby reducing the energy barrier to interfacial peel and shear failure. The weakening effects are exacerbated by the presence of aggressive ions, as Na{sup +} ions attracted to the CSH surface accumulate more water molecules in the interfacial region by forming hydrated ions clusters, which ultimately accelerates the epoxy/CSH interfacial degradation.

36 MATERIALS SCIENCE↗

Non-equilibrium simulations of hydraulic permeation: Role of mechanical boundary conditions in dense membranes

Understanding the mechanisms of water transport in reverse osmosis membranes is critical for improving membrane performance and guiding material design. While classical models describe transport as either solution-diffusion (SD)—involving concentration-driven diffusion through a homogeneous medium—or pore-flow (PF)—involving pressure-driven convection through percolated water channels—their applicability to crosslinked polyamide membranes remains debated. Here, using non-equilibrium molecular dynamics simulations, we investigate the impact of mechanical support conditions on pressure-driven water transport in polyamide membranes across varying crosslink densities and pressure differentials (1000–5000 bar). Two support conditions are considered: graphene-restrained, representing experimentally relevant supported membranes, and freeze-restrained, mimicking a self-supported structure. In graphene-restrained systems, water concentration gradients and constant pressure profiles emerge, consistent with SD theory and incompatible with PF assumptions due to the absence of percolated pores and sub-nanometer voids. In contrast, freeze-restrained systems display uniform water concentration and linearly decreasing pressure at 1000 bar, and exhibit compressibility-induced water gradients and partial percolation at 5000 bar, resembling PF-like behavior. However, the underlying assumptions of PF theory—continuous solvent pathways and pressure transmission through water-filled pores—are not met under most conditions. Our results demonstrate that accurate modeling of reverse osmosis membranes must incorporate realistic mechanical boundary conditions to distinguish between transport mechanisms. For dense polyamide membranes supported by porous substrates, graphene-restrained simulations best reflect experimental setups and support the SD model as the dominant mechanism of water permeation.

molecular dynamics↗

Ab Initio Simulations of Temperature Dependent Phase Stability and Martensitic Transitions in NiTi

For NiTi based alloys, the shape memory effect is governed by a transition from a low-temperature martensite phase to a high-temperature austenite phase. Despite considerable experimental and computational work, basic questions regarding the stability of the phases and the martensitic phase transition remain unclear even for the simple case of binary, equiatomic NiTi. We perform ab initio molecular dynamics simulations to describe the temperature-dependent behavior of NiTi and resolve several of these outstanding issues. Structural correlation functions and finite temperature phonon spectra are evaluated to determine phase stability. In particular, we show that finite temperature, entropic effects stabilize the experimentally observed martensite (B19') and austenite (B2) phases while destabilizing the theoretically predicted (B33) phase. Free energy computations based on ab initio thermodynamic integration confirm these results and permit estimates of the transition temperature between the phases. In addition to the martensitic phase transition, we predict a new transition between the B33 and B19' phases. The role of defects in suppressing these phase transformations is discussed.

nickel titanium↗

Ion density waves driving the formation of filamentary dust structures

The PlasmaKristall-4 (PK-4) experiment on the International Space Station allows for the study of the 3-dimensional interaction between plasma and dust particles. Previous simulations of the PK-4 environment have discovered fast moving ionization waves in the dc discharge. These ionization waves vary the plasma parameters by up to an order of magnitude, which may affect the mechanisms responsible for the self-organization of chains seen in the PK-4 experiment. Here, we adapt a molecular dynamics simulation to employ temporally varying plasma conditions in order to investigate the effect on the dust charging and electrostatic potential. In order to describe the differences between the average of the plasma conditions and the time-varying plasma condition, we present a model to reproduce the interaction that takes into account the negative potential from the dust grain and the positive potential from the ion wake.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Molecular Design Principles for Photosystem I-Based Biohybrid Solar Fuel Catalysts

Direct solar-to-chemical conversion offers a compelling route to clean, dispatchable energy. Photosystem I (PSI), an evolutionarily optimized light-driven oxidoreductase, can be repurposed for solar-fuel production by coupling its photochemistry to catalytic interfaces. However, the molecular determinants that govern productive electron transfer to abiotic catalysts remain poorly understood. Here, we present molecular structures of active PSI-Pt nanoparticle (PtNP) biohybrids that reveal how protein architecture controls catalyst access, binding geometry, and photocatalytic efficiency. Removal of stromal subunits exposes the electron transfer chain and enables PtNP binding proximal to the F X cluster, demonstrating that steric occlusion limits access to native acceptor regions in PSI. In contrast, in trimeric PSI, PtNPs bind at multiple sites per monomer, but only a subset are positioned within electron transfer distance of terminal cofactors, resulting in a heterogeneous population of productive and nonproductive configurations. Structural analyses and molecular dynamics simulations define the interface topology, electrostatics, and cofactor-to-nanoparticle distances that govern catalyst binding and electron transfer. These results establish that catalytic inefficiency arises not only from intrinsic electron transfer constraints but also from the distribution of binding geometries imposed by the protein scaffold. Together, these findings provide a molecular framework linking protein structure to biohybrid function and define design principles for engineering PSI-based solar fuel systems and protein-nanomaterial interfaces for light-driven catalysis.

biohybrid↗

Interplay of molecular dynamics and radiative decay of a TADF emitter in a glass-forming liquid

Herein we investigate the role of molecular dynamics in the luminescent properties of a prototypical thermally activated delayed fluorescence (TADF) emitter, NAI-DMAC, in solution using a combination of temperature dependent time-resolved photoluminescence and absorption spectroscopies. We use a glass forming liquid, 2-methylfuran, to introduce an abrupt change in the temperature dependent diffusion dynamics of the solvent and examine the influence this has on the emission intensity of NAI-DMAC molecules. Comparison of experiment with first principles molecular dynamics simulations reveals that the emission intensity of NAI-DMAC molecules follows the temperature-dependent self-diffusion dynamics of the solvent. A marked reduction of emission intensity is observed as the temperature decreases toward the glass transition because the rate at which NAI-DMAC molecules can access emissive molecular conformations is greatly reduced. Below the glass transition, the diffusion dynamics of the solvent changes more slowly with temperature, which causes the emission intensity to decrease more slowly as well. The combination of experiment and computation suggests a pathway by which TADF emitters may transiently access a distribution of conformational states and avoid the need for an average conformation that strikes a balance between lower singlet–triplet energy splittings versus higher emission probabilities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evaluating the active site-substrate interplay between x-ray crystal structure and molecular dynamics in chorismate mutase

Designing realistic quantum mechanical (QM) models of enzymes is dependent on reliably discerning and modeling residues, solvents, and cofactors important in crafting the active site microenvironment. Interatomic van der Waals contacts have previously demonstrated usefulness toward designing QM-models, but their measured values (and subsequent residue importance rankings) are expected to be influenceable by subtle changes in protein structure. Using chorismate mutase as a case study, this work examines the differences in ligand-residue interatomic contacts between an x-ray crystal structure and structures from a molecular dynamics simulation. Select structures are further analyzed using symmetry adapted perturbation theory to compute ab initio ligand-residue interaction energies. The findings of this study show that ligand-residue interatomic contacts measured for an x-ray crystal structure are not predictive of active site contacts from a sampling of molecular dynamics frames. In addition, the variability in interatomic contacts among structures is not correlated with variability in interaction energies. However, the results spotlight using interaction energies to characterize and rank residue importance in future computational enzymology workflows.

Chemistry↗

Ion Solvation and Hydrogen Bonding in Liquid Electrolytes

The primary goal of the proposed research was to explore the use of far-infrared (FIR) spectroscopy for providing new informal on about the solvation structure and dynamics of small ions such as Li + , Na + , and Mg 2+ in electrolyte solutions commonly used in energy-related applications. Classical and ab initio molecular dynamics simulations were to be carried out together with spectroscopic measurements to aid interpretation of the spectra generated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Coarse-grained molecular dynamics integrated with convolutional neural network for comparing shapes of temperature sensitive bottlebrushes

Quantification of shape changes in nature-inspired soft material architectures of stimuli-sensitive polymers is critical for controlling their properties but is challenging due to their softness and flexibility. Here, we have computationally designed uniquely shaped bottlebrushes of a thermosensitive polymer, poly(N-isopropylacrylamide) (PNIPAM), by controlling the length of side chains along the backbone. Coarse-grained molecular dynamics simulations of solvated bottlebrushes were performed below and above the lower critical solution temperature of PNIPAM. Conventional analyses (free volume, asphericity, etc.) show that lengths of side chains and their immediate environments dictate the compactness and bending in these architectures. We further developed 100 unique convolutional neural network models that captured molecular-level features and generated a statistically significant quantification of the similarity between different shapes. Thus, our study provides insights into the shapes of complex architectures as well as a general method to analyze them. The shapes presented here may inspire the synthesis of new bottlebrushes.

36 MATERIALS SCIENCE↗