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Non-linear Hamiltonian models for DNA
Nucleic acids’ physical properties have been investigated by theoretical methods based both on fully atomistic representations and on coarse-grained...
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A Review of Mechanics-Based Mesoscopic Membrane Remodeling Methods: Capturing Both the Physics and the Chemical Diversity
Specialized classes of proteins, working together in a tightly orchestrated manner, induce and maintain highly curved cellular and organelles...
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Twist-stretch relations in nucleic acids
Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule...
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Multiscale Modeling of Protein-RNA Condensation in and Out of Equilibrium
A vast number of intracellular membraneless bodies also known as biomolecular condensates form through a liquid-liquid phase separation (LLPS) of...
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Simulating 3D Cell Shape with the Cellular Potts Model
Computer simulations have become a widely used method for the field of mechanobiology. An important question is whether one can predict the shape and...
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Nonlinear physics opens a new paradigm for accurate transcription start site prediction
There is evidence that DNA breathing (spontaneous opening of the DNA strands) plays a relevant role in the interactions of DNA with other molecules,...
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Field-Theoretic Simulation Method to Study the Liquid–Liquid Phase Separation of Polymers
Liquid–liquid phase separation (LLPS) is a process that results in the formation of a polymer-rich liquid phase coexisting with a polymer-depleted...
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Patchy Particle Models to Understand Protein Phase Behavior
In this chapter we describe numerical procedures to evaluate the phase behavior of coarse-grained models for globular proteins. Specifically we focus...
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Molecular dynamics simulations in photosynthesis
Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large...
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Adaptive resolution simulations of biomolecular systems
In this review article, we discuss and analyze some recently developed hybrid atomistic–mesoscopic solvent models for multiscale biomolecular...
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Simulating Protein-Mediated Membrane Remodeling at Multiple Scales
The resha** of the cell membrane is integral in many important cellular pathways, such as division, immune response, infection, trafficking, and...
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Cholesterol Effects on the Physical Properties of Lipid Membranes Viewed by Solid-state NMR Spectroscopy
In this chapter, we review the physical properties of lipid/cholesterol mixtures involving studies of model membranes using solid-state NMR...
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Membrane-Mediated Interactions
Interactions mediated by the cell membrane between inclusions, such as membrane proteins or antimicrobial peptides, play important roles in their...
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Simulation of Morphogen and Tissue Dynamics
Morphogenesis, the process by which an adult organism emerges from a single cell, has fascinated humans for a long time. Modeling this process can...
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Adhesion of Biological Membranes
One of the most important triggers of cell activity is adhesion, a process by which cells and their organelles interact and attach to substrates,...
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Molecular Modeling
Recent advances in theoretical methods based on quantum mechanics and classical mechanics with visualization tools have played a very important role...