Related papers: Crowding induced entropy-enthalpy compensation in …
Here, we show by solution nuclear magnetic resonance measurements that the urea-unfolded protein apoazurin becomes elongated when the synthetic crowding agent dextran 20 is present, in contrast to the prediction from the macromolecular…
There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to…
We give an overview exploring the role of kinetics in multicomponent mixtures. Compared to the most commonly studied binary (single species plus solvent) case, multicomponent fluids show a rich interplay between kinetics and thermodynamics…
Macromolecular crowding plays a principal role in a wide range of biological processes including gene expression, chromosomal compaction, and viral infection. However, the impact that crowding has on the dynamics of nucleic acids remains a…
Monte Carlo computer simulations are used to study the segregation behaviour of two polymers under cylindrical confinement. Using a multiple-histogram method, the conformational free energy, F, of the polymers was measured as a function of…
Using confocal microscopy we investigate the effect of attraction on the packing of polydisperse emulsions under gravity. We find that the distributions of neighbors, coordination number, and local packing fraction as a function of…
Extensive molecular dynamics simulations were conducted to explore the conformational phase diagram of a neutral polymer in the presence of attractive crowders of varying sizes. For weakly self-attractive polymers, larger crowders induce a…
We evaluate the entanglement entropy of a single connected region in excited states of one-dimensional massive free theories with finite numbers of particles, in the limit of large volume and region length. For this purpose, we use…
Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial…
Many enhanced sampling methods, such as Umbrella Sampling, Metadynamics or Variationally Enhanced Sampling, rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate collective…
Collective motion in biology is often modelled as a dynamical system, in which individuals are represented as particles whose interactions are determined by the current state of the system. Many animals, however, including humans, have…
Neural circuits must balance local connectivity constraints against the need for global integration. Here we introduce a minimal wiring rule motivated by synaptic crowding: as a neuron accumulates incoming connections, each additional…
We study statistical properties of interacting protein-like surfaces and predict two strong, related effects: (i) statistically enhanced self-attraction of proteins; (ii) statistically enhanced attraction of proteins with similar…
We demonstrate how concepts of statistical mechanics of interacting particles can have important implications in the choice of interaction potentials to model qualitative properties of cell aggregates in theoretical biology. We illustrate…
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…
Experiments show that macromolecular crowding modestly reduces the size of intrinsically disordered proteins (IDPs) even at volume fraction ($\phi$) similar to that in the cytosol whereas DNA undergoes a coil-to-globule transition at very…
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is…
While the impact of crowding on the diffusive transport of molecules within a cell is widely studied in biology, it has thus far been neglected in traffic systems where bulk behavior is the main concern. Here, we study the effects of…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
Based on a reconsideration of the Gibbs paradox, we show that a residual, non-extensive term in entropy turns up upon mixing identical particles, whether they are indistinguishable or not. The positive contribution from this residual…