Related papers: Quantifying the Errors Introduced by Continuum Sca…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
Proton scattering in some water and tissue equivalent phantom materials was measured to evaluate their simulation accuracy of water and respective human biological tissues. The measurements were performed on the medical facility of the ITEP…
Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid domains linked by generalized (rotational and stretching) harmonic springs. We present a method to obtain the elastic parameters and overdamped…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Intrinsically Disordered Proteins (IDPs) perform a broad range of biological functions. Their relevance has motivated intense research activity seeking to characterize their sequence/structure/function relationships. However, the…
Grazing-incidence X-ray diffraction (GIXRD) is a scattering technique which allows one to characterize the structure of fluid interfaces down to the molecular scale, including the measurement of the surface tension and of the interface…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
The lifetime and utilization of a nuclear fusion reactor like ITER depends strongly on its capabilities to mitigate damage during disruptions. While shattered pellet injection (SPI) was chosen as the baseline mitigation method for ITER, the…
Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and many diverging properties. IDPs-and intrinsically disordered regions (IDRs) interspersed between folded domains-are generally characterized as…
We report simulation studies of 33 single intrinsically disordered proteins (IDPs) using coarse-grained (CG) bead-spring models where interactions among different amino acids are introduced through a hydropathy matrix and additional…
We propose an algorithmic strategy for improving the efficiency of Monte Carlo searches for the low-energy states of proteins. Our strategy is motivated by a model of how proteins alter their shapes. In our model when proteins fold under…
We propose to develop mean field theory in combination with Glauber algorithm, to model and interpret protein dynamics and structure formation in small to wide angle x-ray scattering (S/WAXS) experiments. We develop the methodology by…
Many biochemical applications such as molecular property prediction require models to generalize beyond their training domains (environments). Moreover, natural environments in these tasks are structured, defined by complex descriptors such…
Granular media (e.g., cereal grains, plastic resin pellets, and pills) are ubiquitous in robotics-integrated industries, such as agriculture, manufacturing, and pharmaceutical development. This prevalence mandates the accurate and efficient…
Biomaterials such as protein or polysaccharide gels are known to behave qualitatively as soft solids and to rupture under an external load. Combining optical and ultrasonic imaging to shear rheology we show that the failure scenario of a…
The conformational complexity of linear polymers far exceeds that of point-like atoms and molecules. Polymers can bend, twist, even become knotted. Thus they may also display a much richer phase structure than point particles. But it is not…
Liquid cellular compartments spatially segregate from the cytoplasm and can regulate aberrant protein aggregation, a process linked to several medical conditions, including Alzheimer's and Parkinson's diseases. Yet the mechanisms by which…
Irradiation-induced void swelling is a critical degradation mechanism for structural materials in nuclear reactors, dictating component operational lifespan and safety. While recent machine learning (ML) approaches have improved the…
We outline a strategy for quantitatively evaluating the conformational characteristics of self-assembled structures using the techniques of contrast variation small angle neutron scattering. By means of basis function expansion, a case…
Machine-learned coarse-grained (CG) models have the potential for simulating large molecular complexes beyond what is possible with atomistic molecular dynamics. However, training accurate CG models remains a challenge. A widely used…