Saddles in the energy landscape: extensivity and thermodynamic formalism

We formally extend the energy landscape approach for the thermodynamics of liquids to account for saddle points. By considering the extensive nature of macroscopic potential energies, we derive the scaling behavior of saddles with system size, as well as several approximations for the properties of low-order saddles (i.e., those with only a few unstable directions). We then cast the canonical partition function in a saddle-explicit form and develop, for the first time, a rigorous energy landscape approach capable of reproducing trends observed in simulations, in particular the temperature dependence of the energy and fractional order of sampled saddles.Comment: 4 pages, 1 figur

REGULATION OF THE 64-kDA SUBUNIT OF CLEAVAGE STIMULATORY FACTOR ACTIVITY IN MACROPHAGE AND B LYMPHOCYTE mRNA 3'-END PROCESSING

Eukaryotic pre-mRNA is processed within the 3'-untranslated region (3'-UTR) resulting in cleavage and polyadenylation. The efficiency of the cleavage reaction is dependent on the binding activity of the 64-kDa subunit of CstF, CstF-64, to the pre-mRNA and is increased with elevated levels of CstF-64. There is evidence that alternative polyadenylation occurs in the presence of increased CstF-64. Our results showed that CstF-64 levels increased with LPS stimulation of RAW 264.7 macrophages while the expression of other pre-mRNA processing factors remained unchanged. Because of the evidence that several macrophage genes exhibit alternative polyadenylation and post-transcriptional regulation under LPS stimulation, we used a reporter mini-gene to identify alternative polyadenylation in LPS-stimulated RAW macrophages. Upon LPS stimulation we measured a 2.5-fold increase in proximal poly(A) site selection that correlated with elevated levels of CstF-64. Forced expression of CstF-64 demonstrated similar alternative polyadenylation. Microarray analysis demonstrated 515 genes changed expression with LPS stimulation, 15 of which also changed with CstF-64 over-expression. A closer analysis of 5 of these 15 genes demonstrated alternative polyadenylation within their 3'-UTR. Closer analysis of the 3'-UTRs showed putative AU-rich regulatory elements. There is also evidence that pre-mRNA processing is coupled with transcription. Previous work has shown that the carboxy-terminal domain (CTD) of RNAP-II is necessary for 3'-end processing, that CstF binds to RNAP-II CTD and that this binding is CTD phosphorylation dependent. Because our lab has also shown that increases in CstF-64 binding activity upon B-cell differentiation causes alternative polyadenylation on the Ig heavy chain gene and occurs in the absence of CstF-64 increases, we believe that the local concentration of CstF-64 to the nascent pre-mRNA is increased in plasma cells through the phosphorylation-dependent recruitment of CstF-64 to RNAP-II CTD. Using chromatin immunoprecipitation (ChIP), we measured an increase in Serine-2 and Serine-5 phosphorylation of the RNAP-II CTD at the promoter and variable regions of the Ig heavy chain gene in plasma cells compared to memory B cells. We believe that this increase in RNAP-II CTD phosphorylation plays a role in either increased transcription of the Ig heavy chain gene or recruitment of pre-mRNA processing factors to the transcriptional machinery

Optical Parametric Oscillation in Orientation-Patterned Gallium Arsenide

Tunable laser sources in the mid-infrared (MIR) spectral range are required for several Air Force applications. Existing lasers with output in the near-infrared can be converted to more desirable MIR by using nonlinear effects. Orientation patterned gallium arsenide (OPGaAs) is a promising nonlinear conversion material because it has broad transparency and can be engineered for specific pump laser and output wavelengths using quasi-phase matching techniques. This research examines optical parametric oscillation (OPO) of several OPGaAs samples using a 2.052 micrometers wavelength Tm, Ho:YLF pump laser. Of the seven samples available the five that were capable of getting OPO output with this pump were tested and OPO was successfully demonstrated on 4 of the 5. The highest slope efficiency of 10% was seen in sample 5. The highest pump power of incident 190 mW without causing damage to the AR coatings was applied to sample 4. Finally spectroscopic data of input and output was obtained and compared to calculated values

On the Wang-Landau Method for Off-Lattice Simulations in the "Uniform" Ensemble

We present a rigorous derivation for off-lattice implementations of the so-called "random-walk" algorithm recently introduced by Wang and Landau [PRL 86, 2050 (2001)]. Originally developed for discrete systems, the algorithm samples configurations according to their inverse density of states using Monte-Carlo moves; the estimate for the density of states is refined at each simulation step and is ultimately used to calculate thermodynamic properties. We present an implementation for atomic systems based on a rigorous separation of kinetic and configurational contributions to the density of states. By constructing a "uniform" ensemble for configurational degrees of freedom--in which all potential energies, volumes, and numbers of particles are equally probable--we establish a framework for the correct implementation of simulation acceptance criteria and calculation of thermodynamic averages in the continuum case. To demonstrate the generality of our approach, we perform sample calculations for the Lennard-Jones fluid using two implementation variants and in both cases find good agreement with established literature values for the vapor-liquid coexistence locus.Comment: 21 pages, 4 figure

Joe Scott Shell and Christy Burleson in a Junior Recital

This is the program for the junior recital of tenor, Joe Scott Shell, and pianist, Christy Burleson. The recital was held on March 2, 1990, in the Mabee Fine Arts Center Recital Hall

Joe Scott Shell and Shaun Walvoord in a Senior Composition Recital

This is the program for the senior composition recital of Joe Scott Shell and Shaun Walvoord. The recital was held on February 19, 1990, in Mabee Fine Arts Center Recital Hall

Energy landscapes, ideal glasses, and their equation of state

Using the inherent structure formalism originally proposed by Stillinger and Weber [Phys. Rev. A 25, 978 (1982)], we generalize the thermodynamics of an energy landscape that has an ideal glass transition and derive the consequences for its equation of state. In doing so, we identify a separation of configurational and vibrational contributions to the pressure that corresponds with simulation studies performed in the inherent structure formalism. We develop an elementary model of landscapes appropriate to simple liquids which is based on the scaling properties of the soft-sphere potential complemented with a mean-field attraction. The resulting equation of state provides an accurate representation of simulation data for the Lennard-Jones fluid, suggesting the usefulness of a landscape-based formulation of supercooled liquid thermodynamics. Finally, we consider the implications of both the general theory and the model with respect to the so-called Sastry density and the ideal glass transition. Our analysis shows that a quantitative connection can be made between properties of the landscape and a simulation-determined Sastry density, and it emphasizes the distinction between an ideal glass transition and a Kauzmann equal-entropy condition.Comment: 11 pages, 3 figure

Multiscale simulation of ideal mixtures using smoothed dissipative particle dynamics

Smoothed dissipative particle dynamics (SDPD) [P. Español and M. Revenga, Phys. Rev. E 67, 026705 (2003)] is a thermodynamically consistent particle-based continuum hydrodynamics solver that features scale-dependent thermal fluctuations. We obtain a new formulation of this stochastic method for ideal two-component mixtures through a discretization of the advection-diffusion equation with thermal noise in the concentration field. The resulting multicomponent approach is consistent with the interpretation of the SDPD particles as moving volumes of fluid and reproduces the correct fluctuations and diffusion dynamics. Subsequently, we provide a general multiscale multicomponent SDPD framework for simulations of molecularly miscible systems spanning length scales from nanometers to the non-fluctuating continuum limit. This approach reproduces appropriate equilibrium properties and is validated with simulation of simple one-dimensional diffusion across multiple length scales