Role of Specific Cations and Water Entropy on the Stability of Branched DNA Motif Structures

DNA three-way junctions (TWJs) are important intermediates in various cellular processes and are the simplest of a family of branched nucleic acids being considered as scaffolds for biomolecular nanotechnology. Branched nucleic acids are stabilized by divalent cations such as Mg2+, presumably due to condensation and neutralization of the negatively charged DNA backbone. However, electrostatic screening effects point to more complex solvation dynamics and a large role of interfacial waters in thermodynamic stability. Here, we report extensive computer simulations in explicit water and salt on a model TWJ and use free energy calculations to quantify the role of ionic character and strength on stability. We find that enthalpic stabilization of the first and second hydration shells by Mg2+ accounts for 1/3 and all of the free energy gain in 50% and pure MgCl2 solutions, respectively. The more distorted DNA molecule is actually destabilized in pure MgCl2 compared to pure NaCl. Notably, the first shell, interfacial waters have very low translational and rotational entropy (i.e., mobility) compared to the bulk, an entropic loss that is overcompensated by increased enthalpy from additional electrostatic interactions with Mg2+. In contrast, the second hydration shell has anomalously high entropy as it is trapped between an immobile and bulklike layer. The nonmonotonic entropic signature and long-range perturbations of the hydration shells to Mg2+ may have implications in the molecular recognition of these motifs. For example, we find that low salt stabilizes the parallel configuration of the three-way junction, whereas at normal salt we find antiparallel configurations deduced from the NMR. We use the 2PT analysis to follow the thermodynamics of this transition and find that the free energy barrier is dominated by entropic effects that result from the decreased surface area of the antiparallel form which has a smaller number of low entropy waters in the first monolayer.

Design and Application of a new Multiscale Multidirectional Non-subsampled Filter Bank

We propose a new method for design of computationally efficient nonsubsampled multiscale multidirectional filter bank with perfect reconstruction (PR). This filter bank is composed of two nonsubsampled filter banks, for multiscale decomposition and for directional expansion. For multiscale decomposition, we transform the 1-D equivalent subband filters directly into 2-D equivalent subband filters. The computational cost is considerably reduced by avoiding the computation of 2-D convolutions. The multidirectional decomposition utilizes fan filters. A new method for design of 2-D zero phase FIR fan filter transformation function is developed. This method also aids the transformation of a 1-D filter bank to a 2-D multidirectional filter bank. The potential application of the proposed filter bank is illustrated by comparing the image denoising performance of the proposed filter bank with other design method that exist in available literature.

Quantum phases of dimerized and frustrated Heisenberg spin chains with s=1/2, 1 and 3/2: an entanglement entropy and fidelity study

We study here different regions in phase diagrams of the spin-1/2, spin-1 and spin-3/2 one-dimensional antiferromagnetic Heisenberg systems with frustration (next-nearest-neighbor interaction J(2)) and dimerization (delta). In particular, we analyze the behaviors of the bipartite entanglement entropy and fidelity at the gapless to gapped phase transitions and across the lines separating different phases in the J(2)-delta plane. All the calculations in this work are based on numerical exact diagonalizations of finite systems.

Linear Coding Schemes for the Distributed Computation of Subspaces

Let X-1,..., X-m be a set of m statistically dependent sources over the common alphabet F-q, that are linearly independent when considered as functions over the sample space. We consider a distributed function computation setting in which the receiver is interested in the lossless computation of the elements of an s-dimensional subspace W spanned by the elements of the row vector X-1,..., X-m]Gamma in which the (m x s) matrix Gamma has rank s. A sequence of three increasingly refined approaches is presented, all based on linear encoders. The first approach uses a common matrix to encode all the sources and a Korner-Marton like receiver to directly compute W. The second improves upon the first by showing that it is often more efficient to compute a carefully chosen superspace U of W. The superspace is identified by showing that the joint distribution of the {X-i} induces a unique decomposition of the set of all linear combinations of the {X-i}, into a chain of subspaces identified by a normalized measure of entropy. This subspace chain also suggests a third approach, one that employs nested codes. For any joint distribution of the {X-i} and any W, the sum-rate of the nested code approach is no larger than that under the Slepian-Wolf (SW) approach. Under the SW approach, W is computed by first recovering each of the {X-i}. For a large class of joint distributions and subspaces W, the nested code approach is shown to improve upon SW. Additionally, a class of source distributions and subspaces are identified, for which the nested-code approach is sum-rate optimal.

Refining sub-solidus phase relations in the systems CaO-RuO2-SiO2 and CaO-RuO2-V2O5

Sub-solidus phase relations in the ternary systems CaO-RuO2-SiO2 and CaO-RuO2-V2O5 have been refined using thermodynamic data on calcium ruthenates, silicates and vanadates. Tie lines are established by considering Gibbs energy change for exchange reactions. Quaternary oxides have not been detected in these systems. Because of the relatively large entropy associated with phase transition of Ca2SiO4 from olivine to alpha' structure at 1120 K, reversal of one tie line is seen in the system CaO-RuO2-SiO2 between 950 and 1230 K. There is no change in sub-solidus phase relation as a function of temperature in the system CaO-RuO2-V2O5. Since vanadium can exist in several lower oxidation states, the computed sub-solidus phase relations are valid only at high oxygen partial pressures. There is fair agreement between the computed phase diagram and the limited experimental information available for CaO-deficient compositions in the literature. (C) 2013 Elsevier Ltd. All rights reserved.

Entanglement entropy in higher derivative holography

We consider holographic entanglement entropy in higher derivative gravity theories. Recently Lewkowycz and Maldacena 1] have provided a method to derive the equations for the entangling surface from first principles. We use this method to compute the entangling surface in four derivative gravity. Certain interesting differences compared to the two derivative case are pointed out. For Gauss-Bonnet gravity, we show that in the regime where this method is applicable, the resulting equations coincide with proposals in the literature as well as with what follows from considerations of the stress tensor on the entangling surface. Finally we demonstrate that the area functional in Gauss-Bonnet holography arises as a counterterm needed to make the Euclidean action free of power law divergences.

Information content of molecular graph and prediction of gas phase thermal entropy of organic compounds

Entropy is a fundamental thermodynamic property that has attracted a wide attention across domains, including chemistry. Inference of entropy of chemical compounds using various approaches has been a widely studied topic. However, many aspects of entropy in chemical compounds remain unexplained. In the present work, we propose two new information-theoretical molecular descriptors for the prediction of gas phase thermal entropy of organic compounds. The descriptors reflect the bulk and size of the compounds as well as the gross topological symmetry in their structures, all of which are believed to determine entropy. A high correlation () between the entropy values and our information-theoretical indices have been found and the predicted entropy values, obtained from the corresponding statistically significant regression model, have been found to be within acceptable approximation. We provide additional mathematical result in the form of a theorem and proof that might further help in assessing changes in gas phase thermal entropy values with the changes in molecular structures. The proposed information-theoretical molecular descriptors, regression model and the mathematical result are expected to augment predictions of gas phase thermal entropy for a large number of chemical compounds.

Entropy of quantum states: Ambiguities

The von Neumann entropy of a generic quantum state is not unique unless the state can be uniquely decomposed as a sum of extremal or pure states. As pointed out to us by Sorkin, this happens if the GNS representation (of the algebra of observables in some quantum state) is reducible, and some representations in the decomposition occur with non-trivial degeneracy. This non-unique entropy can occur at zero temperature. We will argue elsewhere in detail that the degeneracies in the GNS representation can be interpreted as an emergent broken gauge symmetry, and play an important role in the analysis of emergent entropy due to non-Abelian anomalies. Finally, we establish the analogue of an H-theorem for this entropy by showing that its evolution is Markovian, determined by a stochastic matrix.

Entanglement entropy from the holographic stress tensor

We consider entanglement entropy in the context of gauge/gravity duality for conformal field theories in even dimensions. The holographic prescription due to Ryu and Takayanagi (RT) leads to an equation describing how the entangling surface extends into the bulk geometry. We show that setting to zero, the timetime component of the Brown-York stress tensor evaluated on the co-dimension 1 entangling surface, leads to the same equation. By considering a spherical entangling surface as an example, we observe that the Euclidean actionmethods in AdS/CFT will lead to the RT area functional arising as a counterterm needed to regularize the stress tensor. We present arguments leading to a justification for the minimal area prescription.

ENTANGLEMENT ENTROPY FROM SURFACE TERMS IN GENERAL RELATIVITY

Entanglement entropy in local quantum field theories is typically ultraviolet divergent due to short distance effects in the neighborhood of the entangling region. In the context of gauge/gravity duality, we show that surface terms in general relativity are able to capture this entanglement entropy. In particular, we demonstrate that for 1+1-dimensional (1 + 1d) conformal field theories (CFTs) at finite temperature whose gravity dual is Banados-Teitelboim-Zanelli (BTZ) black hole, the Gibbons-Hawking-York term precisely reproduces the entanglement entropy which can be computed independently in the field theory.

On generalized gravitational entropy, squashed cones and holography

We consider generalized gravitational entropy in various higher derivative theories of gravity dual to four dimensional CFTs using the recently proposed regularization of squashed cones. We derive the universal terms in the entanglement entropy for spherical and cylindrical surfaces. This is achieved by constructing the Fefferman-Graham expansion for the leading order metrics for the bulk geometry and evaluating the generalized gravitational entropy. We further show that the Wald entropy evaluated in the bulk geometry constructed for the regularized squashed cones leads to the correct universal parts of the entanglement entropy for both spherical and cylindrical entangling surfaces. We comment on the relation with the Iyer-Wald formula for dynamical horizons relating entropy to a Noether charge. Finally we show how to derive the entangling surface equation in Gauss-Bonnet holography.

3D flat holography: entropy and logarithmic corrections

We compute the leading corrections to the Bekenstein-Hawking entropy of the Flat Space Cosmological (FSC) solutions in 3D flat spacetimes, which are the flat analogues of the BTZ black holes in AdS(3). The analysis is done by a computation of density of states in the dual 2D Galilean Conformal Field Theory and the answer obtained by this matches with the limiting value of the expected result for the BTZ inner horizon entropy as well as what is expected for a generic thermodynamic system. Along the way, we also develop other aspects of holography of 3D flat spacetimes.

Generative Maximum Entropy Learning for Multiclass Classification

Maximum entropy approach to classification is very well studied in applied statistics and machine learning and almost all the methods that exists in literature are discriminative in nature. In this paper, we introduce a maximum entropy classification method with feature selection for large dimensional data such as text datasets that is generative in nature. To tackle the curse of dimensionality of large data sets, we employ conditional independence assumption (Naive Bayes) and we perform feature selection simultaneously, by enforcing a `maximum discrimination' between estimated class conditional densities. For two class problems, in the proposed method, we use Jeffreys (J) divergence to discriminate the class conditional densities. To extend our method to the multi-class case, we propose a completely new approach by considering a multi-distribution divergence: we replace Jeffreys divergence by Jensen-Shannon (JS) divergence to discriminate conditional densities of multiple classes. In order to reduce computational complexity, we employ a modified Jensen-Shannon divergence (JS(GM)), based on AM-GM inequality. We show that the resulting divergence is a natural generalization of Jeffreys divergence to a multiple distributions case. As far as the theoretical justifications are concerned we show that when one intends to select the best features in a generative maximum entropy approach, maximum discrimination using J-divergence emerges naturally in binary classification. Performance and comparative study of the proposed algorithms have been demonstrated on large dimensional text and gene expression datasets that show our methods scale up very well with large dimensional datasets.

Higher spin entanglement entropy from CFT

We consider free fermion and free boson CFTs in two dimensions, deformed by a chemical potential mu for the spin-three current. For the CFT on the infinite spatial line, we calculate the finite temperature entanglement entropy of a single interval perturbatively to second order in mu in each of the theories. We find that the result in each case is given by the same non-trivial function of temperature and interval length. Remarkably, we further obtain the same formula using a recent Wilson line proposal for the holographic entanglement entropy, in holomorphically factorized form, associated to the spin-three black hole in SL(3, R) x SL(3, R) Chern-Simons theory. Our result suggests that the order mu(2) correction to the entanglement entropy may be universal for W-algebra CFTs with spin-three chemical potential, and constitutes a check of the holographic entanglement entropy proposal for higher spin theories of gravity in AdS(3).

A spectral multiscale method for wave propagation analysis: Atomistic-continuum coupled simulation

In this paper, we present a new multiscale method which is capable of coupling atomistic and continuum domains for high frequency wave propagation analysis. The problem of non-physical wave reflection, which occurs due to the change in system description across the interface between two scales, can be satisfactorily overcome by the proposed method. We propose an efficient spectral domain decomposition of the total fine scale displacement along with a potent macroscale equation in the Laplace domain to eliminate the spurious interfacial reflection. We use Laplace transform based spectral finite element method to model the macroscale, which provides the optimum approximations for required dynamic responses of the outer atoms of the simulated microscale region very accurately. This new method shows excellent agreement between the proposed multiscale model and the full molecular dynamics (MD) results. Numerical experiments of wave propagation in a 1D harmonic lattice, a 1D lattice with Lennard-Jones potential, a 2D square Bravais lattice, and a 2D triangular lattice with microcrack demonstrate the accuracy and the robustness of the method. In addition, under certain conditions, this method can simulate complex dynamics of crystalline solids involving different spatial and/or temporal scales with sufficient accuracy and efficiency. (C) 2014 Elsevier B.V. All rights reserved.