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We consider a one-dimensional matter-wave bright soliton, corresponding to the ground bound state of N particles of mass m having a binary attractive delta potential interaction on the open line. For a full N-body quantum treatment, we…
Elastic electron scattering has been used to paint the most accurate picture of the proton distribution in atomic nuclei. Spurred by new experimental developments, it is now possible to gain valuable insights into the neutron distribution…
A theory is set up of spherical proteins interacting by screened electrostatics and constant adhesion, in which the effective adhesion parameter is optimized by a variational principle for the free energy. An analytical approach to the…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
The mechanical unfolding of an engineered protein composed of eight domains of Ig27 is investigated by using atomic force microscopy. Exploiting a fluctuation relation, the equilibrium free energy as a function of the molecule elongation is…
Energy-based models (EBMs) have experienced a resurgence within machine learning in recent years, including as a promising alternative for probabilistic regression. However, energy-based regression requires a proposal distribution to be…
Energy-based models (EBMs) are a simple yet powerful framework for generative modeling. They are based on a trainable energy function which defines an associated Gibbs measure, and they can be trained and sampled from via well-established…
The diffraction slope parameter is investigated for elastic proton-proton and proton-antiproton scattering based on the all available experimental data at intermediate square of momentum transfer in the main. Energy dependence of the…
We study the enzymatic degradation of an elastic fiber under tension using an an isotropic random-walk model, coupled with binding-unbinding reactions that weaken the fiber. The fiber is represented by a chain of elastic springs in series,…
Many signalling functions in molecular biology require proteins bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit…
For the first time an analytic expression was obtained for the inelastic neutron scattering law with an isotropic neutron source within the gas model, considering moderating medium temperature as a parameter. The inelastic scattering law is…
Optical model potentials for elastic nucleon nucleus scattering are calculated for a number of target nuclides from a full-folding integral of two different realistic target density matrices together with full off-shell nucleon-nucleon…
Jarzynski's equality [1] allows us to investigate free energy landscapes (FELs) by constructing distributions of work performed on a system from an initial ensemble of states to final states. This work is experimentally measured by…
Major advances in large-scale yeast two hybrid (Y2H) screening have provided a global view of binary protein-protein interactions across species as dissimilar as human, yeast, and bacteria. Remarkably, these analyses have revealed that all…
We introduce a novel Earth-like planet surface temperature model (ESTM) for habitability studies based on the spatial-temporal distribution of planetary surface temperatures. The ESTM adopts a surface Energy Balance Model complemented by:…
The diffraction of fast atoms at grazing incidence on crystal surfaces (GIFAD) was first interpreted only in terms of elastic diffraction from a perfectly periodic rigid surface with atoms fixed at equilibrium position. Recently, a new…
Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have…
We demonstrate and characterize a first-principles approach to modeling the mass action dynamics of metabolism. Starting from a basic definition of entropy expressed as a multinomial probability density using Boltzmann probabilities with…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
The charge and magnetic form factors of light nuclei, mainly for mass numbers A<=4, provide a sensitive test of our understanding of nuclei. A number of "exact" calculations of the wave functions starting from the nucleon-nucleon…