Related papers: Sum rules for free energy and frequency distributi…
Periodic patterns play the important regulatory and structural roles in genomic DNA sequences. Commonly, the underlying periodicities should be understood in a broad statistical sense, since the corresponding periodic patterns have been…
The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computational-experimental approach for different lengths of…
We extract values for the free symmetry energy as a function of the fragment size (the proton number Z) from antisymmetrized molecular dynamics (AMD) calculations of calcium collisions. Simple statistical physics describe well the…
The equilibrium structure of a Dinucleosome is studied using an elastic model that takes into account the force and torque balance conditions. Using the proper boundary conditions, it is found that the conformational energy of the problem…
Neutrino mass sum rules relate the three neutrino masses within generic classes of flavour models, leading to restrictions on the effective mass parameter measured in experiments on neutrinoless double beta decay as a function of the…
We evaluate, by means of molecular dynamics simulations employing a realistic DNA coarse-grained model, the phase behaviour and the structural and dynamic properties of tetravalent DNA nanostars, i.e. nanoconstructs completely made of DNA.…
Frequency sum rules are derived in extended quantum systems of non relativistic fermions from a minimal set of assumptions on dynamics in infinite volume, for ground and thermal states invariant under space translations or a lattice…
We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive simplified expressions for the force…
Apparent inconsistencies between different formulations of nucleon sum rules at finite density are resolved through a proper accounting of asymmetries in the spectral functions between positive- and negative-energy states.
The first part of this paper develops a theory for the free energy of lyotropic polymer nematic liquid crystals. We use a continuum model with macroscopic elastic moduli for a polymer nematic phase. By evaluating the partition function,…
We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system…
Measurements of the density dependence of the free symmetry energy in low density clustered matter have been extended using the NIMROD multi-detector at Texas A&M University. Thermal coalescence models were employed to extract densities,…
We used the Transfer-Integral method to compute, with an uncertainty smaller than 5%, the six fundamental characteristic exponents of two dynamical models for DNA thermal denaturation and investigate the validity of the scaling laws. Doubts…
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…
A unified treatment for the existence of free energy in several random energy models is presented. If the sequence of distributions associated with the particle systems obeys a large deviation principle, then the free energy exists almost…
New developments are presented in the framework of the model introduced by the authors in refs. [1,2] and in which nucleotides as well as codons are classified in crystal bases of the quantum group U_q(sl(2)+sl(2)) in the limit q -> 0. An…
Partial sum rules are widely used in physics to separate low- and high-energy degrees of freedom of complex dynamical systems. Their application, though, is challenged in practice by the always finite spectrometer bandwidth and is often…
The free energy functional has recently been proposed as a variational principle for bounded rational decision-making, since it instantiates a natural trade-off between utility gains and information processing costs that can be…
Systematic inaccuracy is inherent in any computational estimate of a non-linear average, due to the availability of only a finite number of data values, N. Free energy differences (DF) between two states or systems are critically important…
Examination of symmetry energy is carried out on the basis of an elementary binding-energy formula. Constraints are obtained on the energy value at the normal nuclear density and on the density dependence of the energy at subnormal…