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Peptides, short chains of amino acids, interact with target proteins, making them a unique class of protein-based therapeutics for treating human diseases. Recently, deep generative models have shown great promise in peptide generation.…
The techniques of data-driven backmapping from coarse-grained (CG) to fine-grained (FG) representation often struggle with accuracy, unstable training, and physical realism, especially when applied to complex systems such as proteins. In…
Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly…
In many applications it is desirable to infer coarse-grained models from observational data. The observed process often corresponds only to a few selected degrees of freedom of a high-dimensional dynamical system with multiple time scales.…
Intrinsically disordered proteins (IDPs) are a subset of proteins that lack stable secondary structure. Given their polymeric nature, previous mean-field approximations have been used to describe the statistical structure of IDPs. However,…
The representation of protein backbone geometry through the discrete nonlinear Schr\"odinger equation provides a theoretical connection between biological structure and integrable systems. Although the global application of this framework…
We analyze the motion of individual beads of a polymer chain using a discrete version of De Gennes' reptation model that describes the motion of a polymer through an ordered lattice of obstacles. The motion within the tube can be evaluated…
We studied structures formed by a single $(AB)_k$ multiblock copolymer chain, in which interaction between A-type beads was purely repulsive, and B-type beads tended to aggregate. We studied how attraction between A-type beads and B-type…
In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community…
We introduce a coarse-grained stochastic network dynamics (CGSND) framework for modeling deformation and rupture in polymer networks. The method replaces explicit molecular dynamics (MD) or coarse-grained molecular dynamics (CGMD) with…
We propose a dynamic coarse-graining (CG) scheme for mapping heterogeneous polymer fluids onto extremely CG models in a dynamically consistent manner. The idea is to use as target function for the mapping a wave-vector dependent mobility…
We consider a discrete model of planar elasticity where the particles, in the reference configuration, sit on a regular triangular lattice and interact through nearest neighbor pairwise potentials, with bonds modeled as linearized elastic…
Folding channels and free-energy landscapes of hydrophobic-polar heteropolymers are discussed on the basis of a minimalistic off-lattice coarse-grained model. We investigate how rearrangements of hydrophobic and polar monomers in a…
We report a simulation study for bottle-brush polymers grafted on a rigid backbone. Using a standard coarse-grained bead-spring model extensive molecular dynamics simulations for such macromolecules under good solvent conditions are…
A new tetrahedral structure model was developed and the geometrical structure of jammed disordered packings of monodisperse spheres with different friction coefficients was systematically characterized. An intrinsic structure feature is…
Increasing the efficiency of materials design and discovery remains a significant challenge, especially given the prohibitively large size of chemical compound space. The use of a chemically transferable coarse-grained model enables…
We address an iterative procedure that can be used to detect coarse-grained hyperbolic unstable equilibria (saddle points) of microscopic simulators when no equations at the macroscopic level are available. The scheme is based on the…
We study the coherent flow of a guided Bose-Einstein condensate incident over a disordered region of length L. We introduce a model of disordered potential that originates from magnetic fluctuations inherent to microfabricated guides. This…
The critical behavior of the contact process in disordered and periodic binary 2d-lattices is investigated numerically by means of Monte Carlo simulations as well as via an analytical approximation and standard mean field theory.…
We study the conformational properties of heteropolymers containing two types of monomers A and B, modeled as self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and…