Daan Frenkel
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View article: Giovanni Ciccotti: a Renaissance physicist
Giovanni Ciccotti: a Renaissance physicist Open
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View article: Receptor clustering tunes and sharpens the selectivity of multivalent binding
Receptor clustering tunes and sharpens the selectivity of multivalent binding Open
The immune system exploits a wide range of strategies to combine sensitivity with selectivity for optimal response. We propose a generic physical mechanism that allows tuning the location and steepness of the response threshold of cellular…
View article: A triad of somatic mutagenesis converges in self-reactive B cells to cause a virus-induced autoimmune disease
A triad of somatic mutagenesis converges in self-reactive B cells to cause a virus-induced autoimmune disease Open
The unexplained association between infection and autoimmune disease is strongest for hepatitis C virus-induced cryoglobulinemic vasculitis (HCV-cryovas). To analyze its origins, we traced the evolution of pathogenic rheumatoid factor (RF)…
View article: Self-replication of A <i>β</i> <sub>42</sub> aggregates occurs on small and isolated fibril sites
Self-replication of A <i>β</i> <sub>42</sub> aggregates occurs on small and isolated fibril sites Open
Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process…
View article: Self-reactive B cells traverse a perfect storm of somatic mutagenesis to cause a virus-induced autoimmune disease
Self-reactive B cells traverse a perfect storm of somatic mutagenesis to cause a virus-induced autoimmune disease Open
Summary The unexplained association between infection and autoimmune disease is strongest for hepatitis C virus-induced cryoglobulinemic vasculitis (HCV-CV). We traced the evolution of the pathogenic rheumatoid factor (RhF) autoantibodies …
View article: Correction: The Lennard-Jones potential: when (not) to use it
Correction: The Lennard-Jones potential: when (not) to use it Open
Correction for ‘The Lennard-Jones potential: when (not) to use it’ by Xipeng Wang et al. , Phys. Chem. Chem. Phys. , 2020, 22 , 10624–10633, https://doi.org/10.1039/C9CP05445F.
View article: Self-replication of A<i>β</i><sub>42</sub>aggregates occurs on small and isolated fibril sites
Self-replication of A<i>β</i><sub>42</sub>aggregates occurs on small and isolated fibril sites Open
Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyse the formation of their own copies. The molecular events behind this fibril surface-mediated process…
View article: Simulations of DNA-Origami Self-Assembly Reveal Design-Dependent Nucleation Barriers
Simulations of DNA-Origami Self-Assembly Reveal Design-Dependent Nucleation Barriers Open
Nucleation is the rate-determining step in the kinetics of many self-assembly processes. However, the importance of nucleation in the kinetics of DNA-origami self-assembly, which involves both the binding of staple strands and the folding …
View article: Data set for the replication package of the paper "Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers"
Data set for the replication package of the paper "Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers" Open
Data set for the replication package of the paper "Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers".
View article: Data set for the replication package of the paper "Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers"
Data set for the replication package of the paper "Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers" Open
Data set for the replication package of the paper "Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers".
View article: Using sequence data to predict the self-assembly of supramolecular collagen structures
Using sequence data to predict the self-assembly of supramolecular collagen structures Open
View article: Data set for the replication package of the paper "Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers"
Data set for the replication package of the paper "Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers" Open
Data set for the replication package of the paper "Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers".
View article: Temperature protocols to guide selective self-assembly of competing structures
Temperature protocols to guide selective self-assembly of competing structures Open
Significance Designing functional materials with switchable properties is a highly sought-after goal in materials science. We investigate the computational design of a multicomponent self-assembly system that can be guided into forming one…
View article: Temperature Protocols to Guide Selective Self-Assembly of Competing Structures
Temperature Protocols to Guide Selective Self-Assembly of Competing Structures Open
Multi-component self-assembly mixtures offer the possibility of encoding multiple target structures with the same set of interacting components. Selective retrieval of one of the stored structures has been attempted by preparing an initial…
View article: Special issue in honour of Michael L. Klein FRS
Special issue in honour of Michael L. Klein FRS Open
The Editors of Molecular Physics are delighted to introduce this special issue of the journal honouring and celebrating the scientific achievements of Michael L. Klein (see Figure 1). The original ...
View article: Challenges in modelling diffusiophoretic transport
Challenges in modelling diffusiophoretic transport Open
The methodology to simulate transport phenomena in bulk systems is well-established. In contrast, there is no clear consensus about the choice of techniques to model cross-transport phenomena and phoretic transport, mainly because some of …
View article: Thermodynamics and kinetics of crystallisation in deeply supercooled Stillinger-Weber silicon
Thermodynamics and kinetics of crystallisation in deeply supercooled Stillinger-Weber silicon Open
We study the kinetics of crystallization in deeply supercooled liquid silicon employing computer simulations and the Stillinger-Weber three body potential. The free energy barriers to crystallisation are computed using umbrella sampling Mo…
View article: Modelling aggregates of cetyltrimethylammonium bromide on gold surfaces using dissipative particle dynamics simulations
Modelling aggregates of cetyltrimethylammonium bromide on gold surfaces using dissipative particle dynamics simulations Open
In this study, we developed a coarse-grained model based on the dissipative particle dynamics (DPD) method to investigate the aggregates of the cetyltrimethylammonium bromide (CTAB) molecules on gold surfaces including nanoparticles. We ad…
View article: Estimation of the equilibrium free energy for glasses using the Jarzynski equality
Estimation of the equilibrium free energy for glasses using the Jarzynski equality Open
The free energy of glasses cannot be estimated using thermodynamic integration as glasses are intrinsically not in equilibrium. We present numerical simulations showing that, in contrast, plausible free-energy estimates of a Kob–Andersen g…
View article: Effect of social distancing on super-spreading diseases: why pandemics modelling is more challenging than molecular simulation
Effect of social distancing on super-spreading diseases: why pandemics modelling is more challenging than molecular simulation Open
The aim of this paper is to present some of the features of the non-Poissonian statistics of the spread of a disease like COVID19 to a community of chemical-physicists, who are more used to particle-based models. We highlight some of the r…
View article: Research data supporting "Effect of truncation on effective reproduction number"
Research data supporting "Effect of truncation on effective reproduction number" Open
The file is an Excel worksheet that can be used to compute the effect reproduction number that results if the tail of a negative binomial distribution withe parameters R and k is truncated at n_t.
View article: Reduced variance analysis of molecular dynamics simulations by linear combination of estimators
Reduced variance analysis of molecular dynamics simulations by linear combination of estimators Open
Building upon recent developments of force-based estimators with a reduced variance for the computation of densities, radial distribution functions, or local transport properties from molecular simulations, we show that the variance can be…
View article: Thermodynamics and kinetics of phase separation of protein-RNA mixtures by a minimal model
Thermodynamics and kinetics of phase separation of protein-RNA mixtures by a minimal model Open
View article: Nano-pump based on exothermic surface reactions
Nano-pump based on exothermic surface reactions Open
We present simulations indicating that it should be possible to construct a switchable nano-scale fluid pump, driven by exothermic surface reactions.
View article: Numerical method for computing the free energy of glasses
Numerical method for computing the free energy of glasses Open
We propose a numerical technique to compute the equilibrium free energy of glasses that cannot be prepared quasireversibly. For such systems, standard techniques for estimating the free energy by extrapolation cannot be used. Instead, we u…
View article: Nano-Pump base on Exothermic Surface Reactions
Nano-Pump base on Exothermic Surface Reactions Open
We present simulations indicating that it should be possible to construct a switchable nano-scale fluid pump, driven by exothermic surface reactions. Such a pump could, for instance, be controlled electro-chemically. In our simulations we …
View article: Computing the Heat Conductivity of Fluids from Density Fluctuations
Computing the Heat Conductivity of Fluids from Density Fluctuations Open
Equilibrium molecular dynamics simulations, in combination with the Green-Kubo (GK) method, have been extensively used to compute the thermal conductivity of liquids. However, the GK method relies on an ambiguous definition of the microsco…
View article: Using Molecular Simulation to Compute Transport Coefficients of Molecular Gases
Using Molecular Simulation to Compute Transport Coefficients of Molecular Gases Open
The existing kinetic theory of gases is based on an analytical approach that becomes intractable for all but the simplest molecules. Here we propose a simple numerical scheme to compute the transport properties of molecular gases in the li…
View article: Using Molecular Simulation to Compute Transport Coefficients of Molecular Gases
Using Molecular Simulation to Compute Transport Coefficients of Molecular Gases Open
The existing kinetic theory of gases is based on an analytical approach that becomes intractable for all but the simplest molecules. Here we propose a simple numerical scheme to compute the transport properties of molecular gases in the li…
View article: Liquid network connectivity regulates the stability and composition of biomolecular condensates with many components
Liquid network connectivity regulates the stability and composition of biomolecular condensates with many components Open
Significance LLPS plays an important role in the spatiotemporal organization of the numerous molecular constituents of living cells, via formation of biomolecular condensates. Our simulations provide predictive rules governing the stabilit…