State functions play important roles in thermodynamics. Different from the process function, such as exchanged heat $\delta Q$ and applied work W$, change of state function can be expressed an exact differential. We prove here that, for a generic thermodynamic system, only inverse temperature, namely $1/T$, serve integration factor Q$. The uniqueness invalidates any attempt to define other asso...

We developed a multistep thermodynamic perturbation method to compute the interfacial free energies by nonequilibrium work measurements with cleaving potential procedure. Using this method, we calculated the interfacial free energies of different crystal orientations for the Lennard-Jones system. Our results are in good agreement with the results by thermodynamic integration method. Compared wi...

Nineteen of the highly conserved residues of Escherichia coli (E. coli) Elongation factor Tu (EF-Tu) that form the binding interface with aa-tRNA were mutated to alanine to better understand how modifying the thermodynamic properties of EF-Tu-tRNA interaction can affect the decoding properties of the ribosome. Comparison of ΔΔG(o) values for binding EF-Tu to aa-tRNA show that the majority of th...

the intermolecular forces between water molecules are of great importance in many areas of chemistry including solvation, solution chemistry, and biochemistry. as a result of this (h2o)n systems have received a great significant of attention, both experimental and theoretical. all calculation of this study are carried out by gaussian 98 soft ware. geometry optimization for each cluster were be ...

the aim of the present study was to prepare new cluster (b6c4si) as an antibiotic carrier. density functional theory (dft) method at the b3lyp level of theory in conjugate with the 6-311g** basis set was used to evaluate the interaction between b6c4si cluster and penicillin. binding parameters, homo, lumo and homo- lumo gap were calculated. results show the ‍ b6c4si homo–lumo gap value of 0.13...

we have used a variational approach to calculate some thermodynamic properties of the quasi-one dimensional liquid 3he such as the energy, entropy, free energy, equation of state and heat capacity at finite temperature. we have employed the lennard-jones potential as the inter-atomic interaction. we have seen that the total energy increases by increasing both temperature and density. as expecte...

The Gibbs conditions of stable thermodynamic equilibrium are formulated for nonlinear thermoelastic materials, based on the constrained minimization of four fundamental thermodynamic potentials. Sufficient conditions for incremental stability are stated in each case. The previously unexplored connections between the second-order variations of thermodynamic potentials are used to establish the c...

A novel method for the calculation of the free energy difference between two states of a molecular system is presented. The method, an extension of thermodynamic integration, treats the coupling parameter k as a variable in an extended Hamiltonian formulation and propagates it with the physical coordinates. In the resulting generalized ensemble, the crossing of barriers in the physical space is...

We review a selection of methods for performing enhanced sampling in 1 molecular dynamics simulations. We consider methods based on collective variable biasing 2 and on tempering, and offer both historical and contemporary perspectives. In collective3 variable biasing, we first discuss methods stemming from thermodynamic integration that 4 use mean force biasing, including the adaptive biasing ...