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We present a computer-assisted approach to coarse-graining the evolutionary dynamics of a system of nonidentical oscillators coupled through a (fixed) network structure. The existence of a spectral gap for the coupling network graph…
Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results indicate that short…
This work presents a systematic methodology for describing the transient dynamics of coarse-grained molecular systems inferred from all-atom simulated data. We suggest Langevin-type dynamics where the coarse-grained interaction potential…
Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins' structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of…
A coarse-grained molecular model, which consists of a spherical particle and an orientation vector, is proposed to simulate lipid membrane on a large length scale. The solvent is implicitly represented by an effective attractive interaction…
A generalization of the ABC model, a one-dimensional model of a driven system of three particle species with local dynamics, is introduced, in which the model evolves under either (i) density-conserving or (ii) nonconserving dynamics. For…
We introduce simple models of genetic regulatory networks and we proceed to the mathematical analysis of their dynamics. The models are discrete time dynamical systems generated by piecewise affine contracting mappings whose variables…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
The key finding in the DNA double helix model is the specific pairing or binding between nucleotides A-T and C-G, and the pairing rules are the molecule basis of genetic code. Unfortunately, no such rules have been discovered for proteins.…
We investigate a celebrated problem of one dimensional tight binding model in the presence of disorder leading to Anderson localization from a novel perspective. A binary disorder is assumed to be created by immobile heavy particles for the…
We consider one-dimensional bosonic chains with a repulsive boson-boson interaction that decays exponentially on large length-scales. This model describes transport of Cooper-pairs in a Josepshon junction array, or transport of magnetic…
Many complex structures and stochastic patterns emerge from simple kinetic rules and local interactions, and are governed by scale invariance properties in combination with effects of the global geometry. We consider systems that can be…
The structure of polyelectrolytes is highly sensitive to small changes in the interactions between its monomers. In particular, interactions mediated by counterions play a significant role, and are affected by both specific molecular…
The mechanics of cohesive or cemented granular materials is complex, combining the heterogeneous responses of granular media, like force chains, with clearly defined material properties. Here, we use a discrete element model (DEM)…
A time-dependent global fiber-bundle model of fracture with continuous damage is formulated in terms of a set of coupled non-linear differential equations. A first integral of this set is analytically obtained. The time evolution of the…
A general scheme, which includes constructions of coarse-grained (CG) models, weighted ensemble dynamics (WED) simulations and cluster analyses (CA) of stable states, is presented to detect dynamical and thermodynamical properties in…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…
Peridynamics provides a versatile tool for fracture modelling in materials where fracture pathways cannot be predicted beforehand, but must be envisaged as an emergent features of the deformation process. One class of materials where this…
We study the equilibrium properties of a single flexible homopolymers where consecutive monomers are represented by impenetrable hard spherical beads tangential to each other, and non-consecutive monomers interact via a square-well…
We describe a simple coarse-grained model which is suited to study lipid layers and their phase transitions. Lipids are modeled by short semiflexible chains of beads with a solvophilic head and a solvophobic tail component. They are forced…