arXiv subjects

Andres R. Tejedor

Publications and source records attributed to Andres R. Tejedor.

4 recordsLinked to original sources

arXiv2026

Roadmap for Condensates in Cell Biology

Biomolecular condensates govern essential cellular processes yet elude description by traditional equilibrium models. This roadmap, distilled from structured discussions at a workshop and reflecting the consensus of its participants, clarifies key concepts for researchers, funding bodies, and journals. After unifying terminology that often separates disciplines, we outline the core physics of condensate formation, review their biological roles, and identify outstanding challenges in nonequilibrium theory, multiscale simulation, and quantitative in-cell measurements. We close with a forward-looking outlook to guide coordinated efforts toward predictive, experimentally anchored understanding and control of biomolecular condensates.

physics.bio-ph↗

arXiv2024

Solid-liquid interfacial free energy from computer simulations: Challenges and recent advances

The theory of interfacial properties in liquid-liquid or liquid-vapour systems is nearly 200 years old. The advent of computational tools has greatly advanced the field, mainly through the use of Molecular Dynamics simulations. Despite the successes and advances in the theory of interfacial phenomena for liquid-liquid systems, the study of solid-liquid interfaces remains a challenge both theoretically and experimentally. The main reason why the treatment of solid-liquid systems has fallen behind that of liquid-liquid systems is that there are complications that arise whenever an interface involving solid systems is considered involving both theory of the solid-liquid interface and the calculations using MD simulations. An example of the former is that, contrary to the liquid-liquid case, the interfacial properties of solids depend on the lattice orientation. The main complications in these calculations arise from the fact that for solids the ``mechanical route'' cannot be used. To overcome this problem, several numerical approaches were proposed. The main purpose of this review is to provide an overview of these different methodologies and to discuss their strengths and weaknesses. We classify these methodologies into two main groups: direct and indirect methods. Direct methods are those that can calculate directly the properties of interfaces, while in indirect approaches the properties of the interface are not the primary result of the simulations. We also included a discussion on the origin of the difficulties in considering solid interfaces from a thermodynamic point of view. In the second part of the review, we discuss two key related topics: nucleation theory and curved interfaces. They both represent an important problem in the study of interfaces and in the context of solid-liquid ones for which the research is still extremely active.

cond-mat.soft↗

arXiv2022

Molecular dynamics simulations of active entangled polymers reptating through a passive mesh

In this work, we explore the dynamics of active entangled chains using molecular dynamics simulations of a modified Kremer-Grest model. The active chains are diluted in a mesh of very long passive linear chains, to avoid constraint release effects, and an active force is applied to the monomers in a way that it imparts a constant polar drift velocity along the primitive path. The simulation results show that, over a wide range of activity values, the conformational properties of the chains and the tubes are not affected, but the dynamics of the chains are severely modified. Despite not having an explicit tube, the simulations verify all the predictions of the theory about all possible observables very accurately, including a diffusion coefficient that becomes independent of the molecular weight at moderate values of the activity. Overall, this work provides novel information on the study of active entangled polymers, giving a route map for studying this phenomenon and an efficient way of obtaining a polar activity that reproduces the physics of the active reptation theory.

cond-mat.soft↗

arXiv2022

Detailed dynamics of discrete Gaussian semiflexible chains with arbitrary stiffness along the contour

We revisit a model of semiflexible Gaussian chains proposed by Winkler \textit{et al}, solve the dynamics of the discrete description of the model and derive exact algebraic expressions for some of the most relevant dynamical observables, such as the mean-square displacement of individual monomers, the dynamic structure factor, the end-to-end vector relaxation and the shear stress relaxation modulus. The mathematical expressions are verified by comparing them with results from Brownian dynamics simulations, reporting an excellent agreement. Then, we generalize the model to linear polymer chains with arbitrary stiffness. In particular, we focus on the case of a linear polymer with stiffness that changes linearly from one end of the chain to the other, and study the same dynamical functions previously presented. We discuss different approaches to check whether a polymer has constant or heterogeneous stiffness along its contour. Overall, this work presents a new insight for a well known model for semiflexible chains and provides tools that can be exploited to compare the predictions of the model with simulations of coarse grained semiflexible polymers.

cond-mat.soft↗