Related papers: Influence of pH and sequence in peptide aggregatio…
The presence of protein aggregates in cells is a known feature of many human age-related diseases, such as Huntington's disease. Simulations using fixed parameter values in a model of the dynamic evolution of expanded polyglutamine (PolyQ)…
The coil-globule transition of hetero-polymer chains is studied here. By means of extensive Molecular Dynamics simulations, we show that the transition is directly linked to the complexity of the chain, which depends on the number of…
Hexapeptides are widely applied as a model system for studying amyloid-forming properties of polypeptides, including proteins. Recently, large experimental databases have become publicly available with amyloidogenic labels. Using these…
We examine the symmetry-breaking effect of fixed constellations of particles on the surface-directed spinodal decomposition of binary blends in the presence of particles whose surfaces have a preferential affinity for one of the components.…
We present an accelerated ``on-the-fly'' coupled-cluster path-integral molecular dynamics (PIMD) method for finite-temperature simulations in which electron correlation and nuclear quantum effects are treated simultaneously. The approach is…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
Hybrid particle-field methods are computationally efficient approaches for modelling soft matter systems. So far applications of these methodologies have been limited to constant volume conditions. Here, we reformulate particle-field…
The associative interaction, such as hydrogen bonding, can bring about versatile functionalities to polymer systems, which has been investigated by tremendous researches, but the fundamental understanding on association process is still…
Function of proteins or a network of interacting proteins often involves communication between residues that are well separated in sequence. The classic example is the participation of distant residues in allosteric regulation.…
Liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is a major undergirding factor in the regulated formation of membraneless organelles in the cell. The phase behavior of an IDP is sensitive to its amino acid…
Activated processes such as protein unfolding are highly sensitive to heterogeneity in the environment. We study a highly simplified model of a protein in a random heterogeneous environment, a model of the in vivo environment. It is found…
Peptides, short chains of amino acid residues, play a vital role in numerous biological processes by interacting with other target molecules, offering substantial potential in drug discovery. In this work, we present PepFlow, the first…
Colloidal gels formed from small attractive particles are commonly used in formulations to keep larger components in suspension. However, despite extensive work characterizing unfilled gels, little is known about how larger inclusions alter…
By means of multicanonical computer simulations, we investigate thermodynamic properties of the aggregation of interacting semiflexible polymers. We analyze a mesoscopic bead-stick model, where nonbonded monomers interact via Lennard-Jones…
The folding of a peptide chain into a three dimensional structure is a thermodynamically driven process such that the chain naturally evolves to form domains of similar amino acids. The formation of this domain occurs by curling the one…
Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a…
A method is formulated, based on combining self-consistent field theory with dynamically corrected transition state theory, for estimating the rates of adsorption and desorption of end-constrained chains (e.g. by crosslinks or…
Revealing possible long-living coherence in ultrafast processes allows detecting genuine quantum mechanical effects in molecules. To investigate such effects from a quantum chemistry perspective, we have developed a method for simulating…
The incredible thermo-mechanical properties of biological materials arise from the microscopic scale due to a complex hierarchical mechanism, regulated by microinstabilities at the molecular level. The description of such complex structures…
We describe a general simulation scheme for assessing the thermodynamic consequences of neglecting many-body effects in coarse-grained models of complex fluids. The method exploits the fact that the asymptote of a simple-to-measure…