Related papers: Mesoscale computational protocols for the design o…
In the last few years, de novo molecular design using machine learning has made great technical progress but its practical deployment has not been as successful. This is mostly owing to the cost and technical difficulty of synthesizing such…
Mesoscale simulations of woven composites using parameterized analytical geometries offer a way to connect constituent material properties and their geometric arrangement to effective composite properties and performance. However, the…
We use density functional theory to describe the phase behaviors of rigid molecules. The construction of kernel function G(x, P, x, P) is discussed. Excluded-volume potential is calculated for two types of molecules with C_{2v} symmetry.…
The properties of the interface in a phase-separated solution of polymers with different degrees of polymerization and Kuhn segment lengths are calculated. The starting point is the planar interface, the profile of which is calculated in…
A hybrid mesoscopic multi-particle collision model is used to study diffusion-influenced reaction kinetics. The mesoscopic particle dynamics conserves mass, momentum and energy so that hydrodynamic effects are fully taken into account.…
Creating a highly parallel and flexible discrete element software requires an interdisciplinary approach, where expertise from different disciplines is combined. On the one hand domain specialists provide interaction models between…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
Cancer is a disease driven by random DNA mutations and the interaction of many complex phenomena. To improve the understanding and ultimately find more effective treatments, researchers leverage computer simulations mimicking the tumor…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Colloidal molecules are designed to mimic their molecular analogues through their anisotropic shape and interactions. However, current experimental realizations are missing the structural flexibility present in real molecules thereby…
Macromolecular crowding affects biophysical processes as diverse as diffusion, gene expression, cell growth, and senescence. Yet, there is no comprehensive understanding of how crowding affects reactions, particularly multivalent binding.…
The behavior of materials is influenced by a wide range of phenomena occurring across various time and length scales. To better understand the impact of microstructure on macroscopic response, multiscale modeling strategies are essential.…
Aligning theoretical atomistic structural models of materials with available experimental data presents a significant challenge for disordered systems. The configurational space to navigate is vast, and faithful realizations require large…
An ensemble of directed macromolecules on a lattice is considered, where the constituting molecules are chosen as a random sequence of N different types. The same type of molecules experiences a hard-core (exclusion) interaction. We study…
Biomolecular condensates constitute a newly recognized form of spatial organization in living cells. Although many condensates are believed to form as a result of phase separation, the physicochemical properties that determine the phase…
The understanding of the type of inhibitory interaction plays an important role in drug design. Therefore, researchers are interested to know whether a drug has competitive or non-competitive interaction to particular protein targets.…
Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer…
We use mesoscale simulations to gain insight into the digestion of biopolymers by studying the break-up dynamics of polymer aggregates (boluses) bound by physical cross-links. We investigate aggregate evolution, establishing that the…
Inhibiting a signalling pathway concerns controlling the cellular processes of a cancer cell's viability, cell division, and death. Assay protocols created to see if the molecular structures of the drugs being tested have the desired…
Studies on random packing of bidispersive particles have shown that such systems can capture the underlying behavior of more complex phenomena found in physics and materials engineering. In industry, bidispersive particles are used to allow…