In systems biology, questions concerning the molecular and cellular makeup of an organism are of utmost importance, especially when trying to understand how unreliable components--like genetic circuits, biochemical cascades, and ion channels, among others--enable reliable and adaptive behaviour. The repertoire and speed of biological computations are limited by thermodynamic or metabolic constr...

The analytical solution of the recently proposed ideal chain polymer mean-spherical approximation (Yu.Kalyuzhnyi, Mol.Phys., 94, 735(1998)) is presented for the multicomponent mixture of charged hardsphere linear chain flexible molecules. The solution apply to any mixture of chain molecules with arbitrary distribution of the charge and size of the beads along the molecular backbone. Closed form...

The thermodynamic properties of Al, Ni, NiAl, and Ni3Al were studied using the first-principles approach. The 0-K total energies are calculated using the ab initio plane wave pseudopotential method within the generalized gradient approximation. The contribution to the free energy from the lattice vibration was calculated using the phonon densities of states derived by means of the ab initio lin...

The free energy and other thermodynamic properties of hexagonal-close-packed iron are calculated by direct ab initio methods over a wide range of pressures and temperatures relevant to the Earth’s core. The ab initio calculations are based on density-functional theory in the generalisedgradient approximation, and are performed using the projector augmented wave (PAW) approach. Thermal excitatio...

Thermodynamic properties of matter generally depend on the details of interactions between its constituent parts. However, in a unitary Fermi gas where the scattering length diverges, thermodynamics is determined through universal functions that depend only on the particle density and temperature. By using only the general form of the equation of state and the equation of force balance, we meas...

Experiments and computer simulations demonstrate that water spontaneously fills the hydrophobic cavity of a carbon nanotube. To gain a quantitative thermodynamic understanding of this phenomenon, we use the recently developed two phase thermodynamics method to compute translational and rotational entropies of confined water molecules inside single-walled carbon nanotubes and show that the incre...

Many engineering problems can be formulated as optimization problems, and the deterministic annealing (DA) method [20] is known as an effective optimization method for such problems. DA is a deterministic variant of simulated annealing (SA) [1, 10]. The DA characterizes the minimization problem of cost functions as the minimization of Helmholtz free energywhich depends on a (pseudo) temperature...

We investigate the elastic and isotropic aggregate properties of ferromagnetic bcc iron as a function of temperature and pressure by computing the Helmholtz free energies for the volume-conserving strained structures using the first-principles linear response linear-muffin-tin-orbital method and the generalized-gradient approximation. We include the electronic excitation contributions to the fr...

We describe a test particle approach based on dynamical density functional theory (DDFT) for studying the correlated time evolution of the particles that constitute a fluid. Our theory provides a means of calculating the van Hove distribution function by treating its self and distinct parts as the two components of a binary fluid mixture, with the "self " component having only one particle, the...

This paper presents a theoretical formalism for describing systems of semiflexible polymers, which can have density variations due to finite compressibility and exhibit an isotropic-nematic transition. The molecular architecture of the semiflexible polymers is described by a continuum wormlike-chain model. The non-bonded interactions are described through a functional of two collective variable...