Generalised expressions for the association and dissociation rate constants of molecules with multiple binding sites

Rate constants for proteins binding to substrates with multiple binding sites using a generalized forward flux sampling expression

(2018) Adithya Vijaykumar et al.   JOURNAL OF CHEMICAL PHYSICS

The opposing effects of isotropic and anisotropic attraction on association kinetics of proteins and colloids

(2017) Arthur C. Newton et al.   JOURNAL OF CHEMICAL PHYSICS

The role of multivalency in the association kinetics of patchy particle complexes

(2017) Arthur C. Newton et al.   JOURNAL OF CHEMICAL PHYSICS

The magnitude of the intrinsic rate constant: How deep can association reactions be in the diffusion limited regime?

(2017) Adithya Vijaykumar et al.   JOURNAL OF CHEMICAL PHYSICS

Foundations and latest advances in replica exchange transition interface sampling

(2017) Raffaela Cabriolu et al.   JOURNAL OF CHEMICAL PHYSICS

Multiscale simulations of anisotropic particles combining molecular dynamics and Green’s function reaction dynamics

(2017) Adithya Vijaykumar et al.   JOURNAL OF CHEMICAL PHYSICS

A thermodynamically consistent model of the post-translational Kai circadian clock

(2017) Joris Paijmans et al.   PLoS Computational Biology

The intrinsic rate constants in diffusion-influenced reactions

(2016) Adithya Vijaykumar et al.   FARADAY DISCUSSIONS

The intrinsic rate constants in diffusion-influenced reactions

(2016) Adithya Vijaykumar et al.   FARADAY DISCUSSIONS

Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

(2015) Adithya Vijaykumar et al.   JOURNAL OF CHEMICAL PHYSICS

New Langevin and gradient thermostats for rigid body dynamics

(2015) R. L. Davidchack et al.   JOURNAL OF CHEMICAL PHYSICS

Rotational diffusion affects the dynamical self-assembly pathways of patchy particles

(2015) Arthur C. Newton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Decoupling circadian clock protein turnover from circadian period determination

(2015) L. F. Larrondo et al.   SCIENCE

Using Markov state models to study self-assembly

(2014) Matthew R. Perkett et al.   JOURNAL OF CHEMICAL PHYSICS

Optimal resource allocation in cellular sensing systems

(2014) Christopher C. Govern et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diffusion modifies the connectivity of kinetic schemes for multisite binding and catalysis

(2013) I. V. Gopich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Viral antigen density and confinement time regulate the reactivity pattern of CD4 T-cell responses to vaccinia virus infection

(2012) V. Vanguri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Processive phosphorylation of ERK MAP kinase in mammalian cells

(2011) K. Aoki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatio-temporal correlations can drastically change the response of a MAPK pathway

(2010) K. Takahashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fundamental Aspects of Protein−Protein Association Kinetics

(2009) G. Schreiber et al.   CHEMICAL REVIEWS

Forward flux sampling for rare event simulations

(2009) Rosalind J Allen et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events

(2008) Weinan E et al.   Annual Review of Physical Chemistry