相关论文: A Two-Step Biopolymer Nucleation Model Shows a Non…
Biomolecular condensates play a crucial role in the spatial organization of living matter. These membrane-less organelles, resulting from liquid-liquid phase separation, operate far from thermodynamic equilibrium, with their size and…
We present a non-isothermal mesoscopic model for investigation of the phase transition dynamics of thermoresponsive polymers. Since this model conserves energy in the simulations, it is able to correctly capture not only the transient…
Heterogeneous distribution of passive and active domains in the chromosome plays a crucial role for its dynamic organization within the cell nucleus. Motivated by that here we investigate the steady-state conformation and dynamics of a…
Polymer models are a widely used tool to study the prebiotic formation of metabolism at the origins of life. Counts of the number of reactions in these models are often crucial in probabilistic arguments concerning the emergence of…
Biological nanomachines are nanometer-size macromolecular complexes that catalyze chemical reactions in the presence of substrate molecules. The catalytic functions carried out by such nanomachines in the cytoplasm, and biological membranes…
Morphological transformations of amphiphilic AB diblock copolymers in mixtures of a common solvent (S1) and a selective solvent (S2) for the B block are studied using the simulated annealing method. We focus on the morphological…
Non-aligning self-propelled particles with purely repulsive excluded volume interactions undergo athermal motility-induced phase separation into a dilute gas and a dense cluster phase. Here, we use enhanced sampling computational methods…
The formation of (bio)molecular condensates via liquid-liquid phase separation in cells has received increasing attention, as these coacervates play important functional and regulatory roles within biological systems. However, the majority…
Recent advances in Generalized Ensemble simulations and microcanonical analysis allowed the investigation of structural transitions in polymer models over a broad range of local bending and torsion strengths. It is reasonable to argue that…
Phase separation, crucial for spatially segregating biomolecules in cells, is well-understood in the simple case of a few components with pairwise interactions. Yet, biological cells challenge the simple picture in at least two ways: First,…
Synthesizing new metal-organic frameworks (MOFs) is a challenging task, as the size, morphology, polymorph and type and number of defects present on the synthesis product may depend on many variables, including temperature, solvent,…
We study the dynamical response of a two-dimensional Ising model subject to a square-wave oscillating external field. In contrast to earlier studies, the system evolves under a so-called soft Glauber dynamic [P.A. Rikvold and M. Kolesik, J.…
We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding quantization, namely, the translocation proceeds…
Systems with long-range interactions when quenced into a metastable state near the pseudo-spinodal exhibit nucleation processes that are quite different from the classical nucleation seen near the coexistence curve. In systems with…
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…
Suspensions of purely repulsive but self-propelled Brownian particles might undergo phase separation, a phenomenon that strongly resembles the phase separation of passive particles with attractions. Here we employ computer simulations to…
We study nonequilibrium dynamical models with two absorbing states: interacting monomer-dimer models, probabilistic cellular automata models, nonequilibrium kinetic Ising models. These models exhibit a continuous phase transition from an…
Homogeneous nucleation of the new phase of one transition near a second phase transition is considered. The system has two phase transitions, we study the nucleation of the new phase of one of these transitions under conditions such that we…
Understanding how glioblastoma (GBM) emerges from initially healthy glial tissue requires models that integrate bioelectrical, metabolic, and multicellular dynamics. This work introduces an ASAL-inspired agent-based framework that simulates…
We discuss the generalization of a classical problem involving an $N$-step ideal polymer adsorption at a sticky boundary (potential well of depth $U$). It is known that as $N$ approaches infinity, the path undergoes a 2nd-order localization…