Calculating potentials of mean force and diffusion coefficients from nonequilibirum processes without Jarzynski's equality

In general, the direct application of the Jarzynski equality (JE) to reconstruct potentials of mean force (PMFs) from a small number of nonequilibrium unidirectional steered molecular dynamics (SMD) paths is hindered by the lack of sampling of extremely rare paths with negative dissipative work. Such trajectories, that transiently violate the second law, are crucial for the validity of JE. As a solution to this daunting problem, we propose a simple and efficient method, referred to as the FR method, for calculating simultaneously both the PMF U(z) and the corresponding diffusion coefficient D(z) along a reaction coordinate z for a classical many particle system by employing a small number of fast SMD pullings in both forward (F) and time reverse (R) directions, without invoking JE. By employing Crook's transient fluctuation theorem (that is more general than JE) and the stiff spring approximation, we show that: (i) the mean dissipative work W_d in the F and R pullings are equal, (ii) both U(z) and W_d can be expressed in terms of the easily calculable mean work of the F and R processes, and (iii) D(z) can be expressed in terms of the slope of W_d. To test its viability, the FR method is applied to determine U(z) and D(z) of single-file water molecules in single-walled carbon nanotubes (SWNTs). The obtained U(z) is found to be in very good agreement with the results from other PMF calculation methods, e.g., umbrella sampling. Finally, U(z) and D(z) are used as input in a stochastic model, based on the Fokker-Planck equation, for describing water transport through SWNTs on a mesoscopic time scale that in general is inaccessible to MD simulations.Comment: ReVTeX4, 13 pages, 6 EPS figures, Submitted to Journal of Chemical Physic

Theoretical prediction of spectral and optical properties of bacteriochlorophylls in thermally disordered LH2 antenna complexes

A general approach for calculating spectral and optical properties of pigment-protein complexes of known atomic structure is presented. The method, that combines molecular dynamics simulations, quantum chemistry calculations and statistical mechanical modeling, is demonstrated by calculating the absorption and circular dichroism spectra of the B800-B850 BChls of the LH2 antenna complex from Rs. molischianum at room temperature. The calculated spectra are found to be in good agreement with the available experimental results. The calculations reveal that the broadening of the B800 band is mainly caused by the interactions with the polar protein environment, while the broadening of the B850 band is due to the excitonic interactions. Since it contains no fitting parameters, in principle, the proposed method can be used to predict optical spectra of arbitrary pigment-protein complexes of known structure.Comment: ReVTeX4, 11 pages, 9 figures, submitted to J. Chem. Phy

Fluctuation-Driven Molecular Transport in an Asymmetric Membrane Channel

Channel proteins, that selectively conduct molecules across cell membranes, often exhibit an asymmetric structure. By means of a stochastic model, we argue that channel asymmetry in the presence of non-equilibrium fluctuations, fueled by the cell's metabolism as observed recently, can dramatically influence the transport through such channels by a ratchet-like mechanism. For an aquaglyceroporin that conducts water and glycerol we show that a previously determined asymmetric glycerol potential leads to enhanced inward transport of glycerol, but for unfavorably high glycerol concentrations also to enhanced outward transport that protects a cell against poisoning.Comment: REVTeX4, 4 pages, 3 figures; Accepted for publication in Phys. Rev. Let

Comment on "T-dependence of the magnetic penetration depth in unconventional superconductors at low temperatures: Can it be linear?"

We show that the clean superconductor with line of gap nodes is not in conflict with the Nernst theorem. The answer to the question in the title of the Schopohl-Dolgov paper in Phys. Rev. Lett. 80 (1998) 4761 (cond-mat/9802264) is yes.Comment: Comment to the paper by Schopohl and Dolgov in Phys. Rev. Lett. 80 (1998) 4761 (cond-mat/9802264), RevTex file, 1 page, no figures, typos are corrected, submitted to Phys. Rev. Let

Pairing Fluctuation Theory of Superconducting Properties in Underdoped to Overdoped Cuprates

We propose a theoretical description of the superconducting state of under- to overdoped cuprates, based on the short coherence length of these materials and the associated strong pairing fluctuations. The calculated $T_c$ and the zero temperature excitation gap $\Delta(0)$, as a function of hole concentration $x$, are in semi-quantitative agreement with experiment. Although the ratio $T_c/\Delta(0)$ has a strong $x$ dependence, different from the universal BCS value, and $\Delta(T)$ deviates significantly from the BCS prediction, we obtain, quite remarkably, quasi-universal behavior, for the normalized superfluid density $\rho_s(T)/\rho_s(0)$ and the Josephson critical current $I_c(T)/I_c(0)$, as a function of $T/T_c$. While experiments on $\rho_s(T)$ are consistent with these results, future measurements on $I_c(T)$ are needed to test this prediction.Comment: 4 pages, 3 figures, REVTeX, submitted to Phys. Rev. Let

Kinetic Monte Carlo and Cellular Particle Dynamics Simulations of Multicellular Systems

Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of cell aggregates as bioink particles. Computer simulations based on Metropolis Monte Carlo (MMC) algorithms were successful in explaining and predicting the resulting stationary structures (corresponding to the lowest adhesion energy state). Here we present two alternatives to the MMC approach for modeling cellular motion and self-assembly: (1) a kinetic Monte Carlo (KMC), and (2) a cellular particle dynamics (CPD) method. Unlike MMC, both KMC and CPD methods are capable of simulating the dynamics of the cellular system in real time. In the KMC approach a transition rate is associated with possible rearrangements of the cellular system, and the corresponding time evolution is expressed in terms of these rates. In the CPD approach cells are modeled as interacting cellular particles (CPs) and the time evolution of the multicellular system is determined by integrating the equations of motion of all CPs. The KMC and CPD methods are tested and compared by simulating two experimentally well known phenomena: (1) cell-sorting within an aggregate formed by two types of cells with different adhesivities, and (2) fusion of two spherical aggregates of living cells.Comment: 11 pages, 7 figures; submitted to Phys Rev

Comment on "Is the nonlinear Meissner effect unobservable?"

In a recent Letter (Phys. Rev. Lett. 81, p.5640 (1998), cond-mat/9808249 v3), it was suggested that nonlocal effects may prevent observation of the nonlinear Meissner effect in YBCO. We argue that this claim is incorrect with regards to measurements of the nonlinear transverse magnetic moment, and that the most likely reason for a null result lies elsewhere.Comment: 1 pag

Non-Locality and Strong Coupling in the Heavy Fermion Superconductor CeCoIn5_{5}: A Penetration Depth Study

We report measurements of the magnetic penetration depth $\lambda$ in single crystals of CeCoIn$_{5}$ down to $\sim$0.14 K using a tunnel-diode based, self-inductive technique at 28 MHz. While the in-plane penetration depth tends to follow a power law, $\lambda_{//} \sim {\it T}^{3/2}$, the data are better described as a crossover between linear ({\it T} $\gg$ ${\it T}^\ast$) and quadratic ({\it T} $\ll {\it T}^\ast$) behavior, with ${\it T}^\ast$ the crossover temperature in the strong-coupling limit. The {\it c}-axis penetration depth $\lambda_{\perp}$ is linear in {\it T}, providing evidence that CeCoIn$_{5}$ is a {\it d}-wave superconductor with line nodes along the {\it c}-axis. The different temperature dependences of $\lambda_{//}$ and $\lambda_{\perp}$ rule out impurity effects as the source of ${\it T}^{\ast}$.Comment: 4 pages, 3 figure

On the T-dependence of the magnetic penetration depth in unconventional superconductors at low temperatures: can it be linear?

We present a thermodynamics argument against a strictly linear temperature dependence of the magnetic penetration depth, which applies to superconductors with arbitrary pairing symmetry at low temperatures.Comment: 5 pages, expanded version of cond-mat/971102

Absence of non-linear Meissner effect in YBa2Cu3O6.95

We present measurements the field and temperature dependence of the penetration depth (lambda) in high purity, untwinned single crystals of YBa2Cu3O6.95 in all three crystallographic directions. The temperature dependence of lambda is linear down to low temperatures, showing that our crystals are extremely clean. Both the magnitude and temperature dependence of the field dependent correction to lambda however, are considerably different from that predicted from the theory of the non-linear Meissner effect for a d-wave superconductor (Yip-Sauls theory). Our results suggest that the Yip-Sauls effect is either absent or is unobservably small in the Meissner state of YBa2Cu3O6.95.Comment: 4 pages, 4 figures (Latex file + Postscipt figures