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Entropy (0):
Recent article
Entropy
Abstract
We start by reproducing the trend in the measured change in catalysis upon mutations (which was assumed to arise as a result of a "dynamical knockout" caused by the mutations). This analysis is performed by calculating the change in the corresponding activation barriers without the need to invoke dy...
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PMID: 21831831
PDF is available here.
PDF is available here.
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Abstract
We present details of our conformationally flexible, 1,3-diamine-tethered guanidine/bisthiourea organocatalysts for chemo-, regio-, and enantioselective 1,4-type Friedel-Crafts reactions of phenols. These organocatalysts show a unique stereo-discrimination governed by the differential activation ent...
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PMID: 21761571
PDF is available here.
PDF is available here.
Abstract
We show that AID inhibits the catalytic function by restraining the KD into an unproductive open conformation, thereby limiting local structural rearrangements, while mutations that disrupt the interactions between the KD and AID allow for both the local structural rearrangement and global interlobe...
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PMID: 21814500
PDF is available here.
PDF is available here.
Abstract
We present an approach, framed in information theory, to assess nonlinear causality between the subsystems of a whole stochastic or deterministic dynamical system. The approach follows a sequential procedure for nonuniform embedding of multivariate time series, whereby embedding vectors are built pr...
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PMID: 21728495
PDF is available here.
PDF is available here.
Abstract
These results are in close agreement with pathophysiological fundamentals and suggest that the airflow pattern becomes less complex in asthmatic patients, which may reduce the adaptability of the respiratory system to perform the exercise that is associated with daily life activities. This analysis...
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PMID: 21565988
PDF is available here.
PDF is available here.
Abstract
We report a first atomistic and statistical analysis of the unfolding of the pseudoknot within gene 32 mRNA of bacteriophage T2. Multiple unfolding pathways, diverse transition states, and various intermediate structures were observed. Water molecules were found to be coupled with the unfolding proc...
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PMID: 21500824
PDF is available here.
PDF is available here.
Abstract
In Taiwan many factors, whether geological parent materials, human activities, and climate change, can affect the groundwater quality and its stability. This work combines factor analysis and kriging with information entropy theory to interpret the stability of groundwater quality va...
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PMID: 21695030
PDF is available here.
PDF is available here.
Abstract
We report in this article the first systematic molecular dynamics investigation of block copolymer thin film ordering for unconfined films. We investigate the molecular basis of the formation of a number of experimentally relevant coating features, including surface islands and vertical lamellae. Su...
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PMID: 21395316
PDF is available here.
PDF is available here.
Abstract
We propose a simple complexity indicator of classical Liouvillian dynamics, namely the separability entropy, which determines the logarithm of an effective number of terms in a Schmidt decomposition of phase space density with respect to an arbitrary fixed product basis. We show that linear growth o...
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PMID: 21517471
PDF is available here.
PDF is available here.
Abstract
We explore the conformational change of the β subunit using all-atom free energy simulations with explicit solvent and propose a detailed mechanism for the conformational change. The β subunit conformational change is accomplished roughly in two characteristic steps: changing of the hydrogen-bond...
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PMID: 21341660
PDF is available here.
PDF is available here.
Abstract
When a monolayer of hard microscale square platelets, produced lithographically, is osmotically concentrated in a flat plane to raise the particle area fraction Φ(A), an order-order transition occurs between a hexagonal rotator crystal and a rhombic crystal. Strikingly, phases having fourfold symmet...
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PMID: 21282614
PDF is available here.
PDF is available here.
Abstract
We provide an overview of its open source implementation based on the Insight Toolkit of the National Institutes of Health. Characterization of the proposed framework includes comparison with other state of the art kernel-based methods and demonstration of its utility for lung registration via label...
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PMID: 20937578
PDF is available here.
PDF is available here.
Biopolymers (95)4 2011
Abstract
We apply size-exclusion chromatography, an entropically controlled technique, to determine the solution conformational entropy (ΔS) of various oligosaccharide series. The aim of the present study is to highlight how, for a given anomeric configuration, glycosidic linkage affects ΔS, and to do so q...
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PMID: 21280018
PDF is available here.
PDF is available here.
Biopolymers (95)4 2011
Abstract
We offer an alternative view that removes the need for sequence-context parameterization by focusing on individual microsopic interactions within a free energy decomposition and explicitly account for nonadditivity in conformational entropy through network rigidity using a Distance Constraint Model...
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PMID: 21280020
PDF is available here.
PDF is available here.
Functional Neurology (26)1 2011
Abstract
Monitoring the level of consciousness in brain-injured patients with disorders of consciousness is crucial as it provides diagnostic and prognostic information. Behavioral assessment remains the gold standard for assessing consciousness but previous studies have shown a high rate of misdiagnosis. Thi...
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PMID: 21693085
PDF is available here.
PDF is available here.
Abstract
Abstract
We complemented stride related measures with measures that quantify trunk movement patterns as indicators of dynamic balance ability during walking. The aim of the study was to quantify the effect of impaired cognition and dual tasking on gait variability and stability in geriatric patients....
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PMID: 21241487
PDF is available here.
PDF is available here.
Abstract
Living systems use information and energy to maintain stable entropy while far from thermodynamic equilibrium. The underlying first principles have not been established.
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PMID: 21818295
PDF is available here.
PDF is available here.
Abstract
Sex differences in response to noxious stimuli or analgesia have been demonstrated. We investigated sex differences in conscious sedation during upper gastrointestinal panendoscopic examination with regard to drug dose and entropy scores.
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PMID: 21316012
PDF is available here.
PDF is available here.
Abstract
We compare results obtained through this explicit water molecule approach to those obtained by means of continuum methods. Car-Parrinello molecular dynamics (CPMD) simulations of the proton-transfer process in bulk with explicit water molecules have been conducted at room temperature. No spontaneous...
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PMID: 21141855
PDF is available here.
PDF is available here.
Abstract
We used computational methods to study the formation of the putative AmB/sterol complexes in a lipid bilayer. The free energy profiles for the AmB-sterol association in phospholipid bilayers containing 30 mol % of sterols were calculated and thoroughly analyzed. The results obtained confirm the form...
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PMID: 21126070
PDF is available here.
PDF is available here.
Abstract
We use Langevin dynamics to investigate the role played by the recently discovered force-induced entropic energy barrier on the two-state hopping phenomena that has been observed in single RNA, DNA and protein molecules placed under a stretching force. Simple considerations about the free energy of...
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PMID: 21050839
PDF is available here.
PDF is available here.
Abstract
We explore the alternation of short protein-coding segments with long noncoding spacers in entire chromosomes, focusing on the scaling properties of block entropy. In previous studies, it has been shown that the sizes of noncoding spacers follow power-law-like distributions in most chromosomes of eu...
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PMID: 21230510
PDF is available here.
PDF is available here.
Abstract
Abstract
We carried out simulations in both gas and aqueous phases by using the ab initio molecular dynamics technique equipped with the method of constraint. The simulations provide relatively complete free-energy information, from which the coexisting coordination pictures are clearly revealed. In both pha...
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PMID: 20657900
PDF is available here.
PDF is available here.
Abstract
We estimate the negative excess entropy (DeltaS(E)) of aqueous methanol at low temperature and high pressure using experimentally-derived structural data and a recently introduced cluster model. On cooling to 190 K the cluster sizes increase, but the change in DeltaS(E), which according to this meth...
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PMID: 20539889
PDF is available here.
PDF is available here.
Abstract
We show, by developing mathematical tools that merge control and information theory with physical chemistry, that seemingly mild constraints on these rates place severe limits on the ability to suppress molecular fluctuations. Specifically, the minimum standard deviation in abundances decreases with...
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PMID: 20829788
PDF is available here.
PDF is available here.
Abstract
Maximum entropy (maxent) models assign probabilities to states that (1) agree with measured macroscopic constraints on attributes of the states and (2) are otherwise maximally uninformative and are thus as close as possible to a specified prior distribution. Such models have recently become popular...
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PMID: 20957971
PDF is available here.
PDF is available here.
Meat Science (86)1 2010
Abstract
As myofibrils consist of a three-dimensional network of long, solid protein particles with the shortest dimension of less than 20 nm, the theoretical foundations of water-holding in meat should be studied from a colloid or surface chemistry point of view. The classical hypotheses for water-holding i...
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PMID: 20627421
PDF is available here.
PDF is available here.
Clinical Neurophysiology (121)9 2010
Abstract
MSE measures identified an abnormal complexity profile across different temporal scales and their relation to the severity of AD. SIGNIFICANCE: These findings indicate that entropy-based analytic methods with applied at temporal scales may serve as a complementary approach for characterizing and und...
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PMID: 20400371
PDF is available here.
PDF is available here.
Abstract
We examined complexity in 8 patients with intracranial hippocampal electrodes during performance of memory tasks (scene encoding and recognition) known to be sensitive to mesial temporal integrity. Our patients were shown to have right mesial temporal seizure onsets, permitting us to evaluate both e...
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PMID: 21175015
PDF is available here.
PDF is available here.
Abstract
The conformational space available to the flexible molecule α-D-Manp-(1-->2)-α-D-Manp-OMe, a model for the α-(1-->2)-linked mannose disaccharide in N- or O-linked glycoproteins, is determined using experimental data and molecular simulation combined with a maximum entropy approach that leads to a...
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PMID: 20574564
PDF is available here.
PDF is available here.
Abstract
Successful industrial use of amylases requires that they are sufficiently stable and active at application conditions, e.g., at high temperature in starch-liquefaction process. In the present study, site-directed mutagenesis was used to enhance the thermal stability and calcium independency of a mes...
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PMID: 20177823
PDF is available here.
PDF is available here.
Abstract
We analysed the scale-dependent structure of cortical interactions by using maximum entropy models to characterize multiple-tetrode recordings from primary visual cortex of anaesthetized macaque monkeys (Macaca mulatta). We compared the properties of firing patterns among local clusters of neurons (...
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PMID: 20601940
PDF is available here.
PDF is available here.
Abstract
We present a small-scale device that directly generates electrical power from the sequential flow of fresh and saline water, without the need for auxiliary processes or converters. The device consists of a sandwich of porous "supercapacitor" electrodes, ion-exchange membranes, and a spacer and can b...
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PMID: 20568741
PDF is available here.
PDF is available here.
Minerva anestesiologica (76)7 2010
Abstract
FEBS Letters (584)13 2010
Abstract
The idea that tunneling is enhanced by the compression of the donor-acceptor distance has attracted significant interest. In particular, recent studies argued that this proposal is consistent with pressure effects on enzymatic reactions, and that the observed pressure effects support the idea of vib...
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PMID: 20433839
PDF is available here.
PDF is available here.
Abstract
Optic Flow (OF) plays an important role in human locomotion and manipulation of OF characteristics can cause changes in locomotion patterns. The purpose of the study was to investigate the effect of the velocity of optic flow on the amount and structure of gait variability. Each subject underwent fo...
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PMID: 20587300
PDF is available here.
PDF is available here.
Abstract
The entropy conservation framework describes the task-organism-environment system as a system where entropy remains a conserved quantity that is redistributed for the purposes of motor adaptation. In this paper, potential applications for the entropy conservation framework in the areas of ergonomics...
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PMID: 20587303
PDF is available here.
PDF is available here.
Development (137)14 2010
Abstract
We derive gene interaction networks for anterior-posterior (AP) patterning under two developmental paradigms. For patterning during growth (paradigm I), which is appropriate for vertebrates and short germ-band insects, the algorithm creates gene expression patterns reminiscent of Hox gene expression...
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PMID: 20570938
PDF is available here.
PDF is available here.
The Journal of Chemical Physics (132)22 2010
Abstract
We develop a statistical mechanical model for the thermal and volumetric properties of waterlike fluids. Each water molecule is a two-dimensional disk with three hydrogen-bonding arms. Each water interacts with neighboring waters through a van der Waals interaction and an orientation-dependent hydro...
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PMID: 20550408
PDF is available here.
PDF is available here.
Nucleic Acids Research (38)11 2010
Abstract
We investigated the thermodynamic stability of the temperature labile hairpin 2 of the Salmonella fourU RNA thermometer over a broad temperature range and determined free energy, enthalpy and entropy values for the base-pair opening of individual nucleobases by measuring the temperature dependence o...
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PMID: 20211842
PDF is available here.
PDF is available here.
Physical Review Letters (104)21 2010
Abstract
We show that entropy production can characterize the behavior of such nonequilibrium systems. To this end we calculate the entropy production for a population model that displays nonequilibrium behavior resulting from cyclic competition. At a critical point the dynamics exhibits a transition from la...
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PMID: 20867139
PDF is available here.
PDF is available here.
Abstract
We use an information theoretic approach to characterize gene expression quantified as mRNA levels in primary keratinocytes (K) and human papillomavirus 16 (HPV16)-transformed keratinocytes (HF1 cells) from early (E) and late (L) passages and from benzo(a)pyrene-treated (BP) L cells. Our starting po...
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PMID: 20479229
PDF is available here.
PDF is available here.
Abstract
We address the structure-function relationship that governs accommodation using all-atom molecular simulations and single-molecule fluorescence resonance energy transfer (smFRET). Simulations that employ an all-atom, structure-based (Gō-like) model illuminate the interplay between configurational e...
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PMID: 20427512
PDF is available here.
PDF is available here.
Abstract
The aqueous solubility of a diatomic molecule as a function of its size & electronegativity difference is investigated. The electronegativity of a diatomic molecule will be calculated using five different electronegativity scales, namely, Pauling [1], Allred-Rochow [2], Mulliken [3,...
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PMID: 20461425
PDF is available here.
PDF is available here.
Abstract
We present an optimized energy function to predict the binding free energy (DeltaDeltaG) of PDZ domain/peptide interactions computationally. Geometry-optimized models of PDZ domain/peptide interfaces were built using ROSETTA: , and protein and peptide side chain and backbone degrees of freedom are m...
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PMID: 20461427
PDF is available here.
PDF is available here.
Abstract
We show that similar results can be found in excitable cluster of ligand-gated calcium channels. Furthermore, we demonstrate that the periodicity of spontaneous Ca2+ spikes elicited by the cluster reveals multiple maxima at small discrete cluster sizes....
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PMID: 20866267
PDF is available here.
PDF is available here.
Abstract
The mean electroglottogram approximate entropy of the normal volunteers was 0.302 (range 0.05-0.42). The mean electroglottogram approximate entropy of the glottic squamous cell carcinoma patients was significantly lower prior to treatment, at 0.227 (range 0.001-0.397; p < 0.0005), but improved after...
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PMID: 20128940
PDF is available here.
PDF is available here.
Abstract
Abstract
We observed that the variety of associations between PDZ and other domains expands greatly along the stem leading to metazoans and choanoflagellates. We asked whether the expansion of PDZ domains was due to random or specific sequence changes. Studying the sequence signatures of 58 PDZ lineages that...
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PMID: 20026484
PDF is available here.
PDF is available here.
Abstract
We demonstrate that these experiments can be replaced by a single 4D experiment that is time-efficient, yields excellent resolution, and captures unique carbon-proton connectivity information. The approach is made practical by the use of non-uniform sampling in the three indirect time dimensions and...
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PMID: 20299257
PDF is available here.
PDF is available here.
Abstract
We use approximate entropy and hydrophobicity patterns to predict G-protein-coupled receptors. Adaboost classifier is adopted as the prediction engine. A low homology dataset is used to validate the proposed method. Compared with the results reported, the successful rate is encouraging. The source c...
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PMID: 19594431
PDF is available here.
PDF is available here.
Abstract
We have is small, the most common size in European enterprises, we used the maximum entropy principle to explore the emotions that are involved in the psychosocial risks. The analyses show that this method takes advantage of the limited information available and guarantee an optimal estimation, the...
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PMID: 20480699
PDF is available here.
PDF is available here.
Journal of Molecular Biology (398)1 2010
Abstract
We analyzed subunit interfaces in 315 homodimers with an X-ray structure in the Protein Data Bank, validated by checking the literature for data that indicate that the proteins are dimeric in solution and that, in the case of the "weak" dimers, the homodimer is in equilibrium with the monomer. The i...
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PMID: 20156457
PDF is available here.
PDF is available here.
Abstract
Burst suppression (BS) activity in EEG is clinically accepted as a marker of brain dysfunction or injury. Experimental studies in a rodent model of brain injury following asphyxial cardiac arrest (CA) show evidence of BS soon after resuscitation, appearing as a transitional recovery pattern between i...
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PMID: 19695982
PDF is available here.
PDF is available here.
Abstract
Emergency response (ER) teams can be formal or ad hoc citizen groups that respond to natural disasters or sentient attackers. This article examines the emergence of leaders in ER teams as a nonlinear dynamical process by which a group that is in a high state of entropy self-organizes into a social s...
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PMID: 20346262
PDF is available here.
PDF is available here.
Neural Computation (22)4 2010
Abstract
We propose here to estimate the entropy rate of a spike train from an inhomogeneous hidden Markov model of the spike intervals. The model is constructed by building a context tree structure to lay out the conditional probabilities of various subsequences of the spike train. For each state in the Mar...
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PMID: 19922298
PDF is available here.
PDF is available here.
Abstract
Recent experiments with amyloid-beta (Abeta) peptides indicate that the formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depend on their structure, which is governed by assembly dynamics. However, a detailed knowledge...
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PMID: 20428075
PDF is available here.
PDF is available here.
Abstract
I and mixed type inhibition of II on both activities of MT. The inhibition constant (K(I)) of II was smaller than that of I. Raising the temperature from 27 to 37 degrees C caused a decrease in K(I) values of I and an increase in values of II. The binding process for inhibition of I was only entropy...
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PMID: 19663663
PDF is available here.
PDF is available here.