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https://www.readbyqxmd.com/read/29149090/computational-methods-for-modeling-aptamers-and-designing-riboswitches
#1
REVIEW
Sha Gong, Yanli Wang, Zhen Wang, Wenbing Zhang
Riboswitches, which are located within certain noncoding RNA region perform functions as genetic "switches", regulating when and where genes are expressed in response to certain ligands. Understanding the numerous functions of riboswitches requires computation models to predict structures and structural changes of the aptamer domains. Although aptamers often form a complex structure, computational approaches, such as RNAComposer and Rosetta, have already been applied to model the tertiary (three-dimensional (3D)) structure for several aptamers...
November 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29141424/stationary-state-distribution-and-efficiency-analysis-of-the-langevin-equation-via-real-or-virtual-dynamics
#2
Dezhang Li, Xu Han, Yichen Chai, Cong Wang, Zhijun Zhang, Zifei Chen, Jian Liu, Jiushu Shao
Langevin dynamics has become a popular tool to simulate the Boltzmann equilibrium distribution. When the repartition of the Langevin equation involves the exact realization of the Ornstein-Uhlenbeck noise, in addition to the conventional density evolution, there exists another type of discrete evolution that may not correspond to a continuous, real dynamical counterpart. This virtual dynamics case is also able to produce the desired stationary distribution. Different types of repartition lead to different numerical schemes, of which the accuracy and efficiency are investigated through studying the harmonic oscillator potential, an analytical solvable model...
November 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29140486/the-national-cancer-institute-s-conference-on-acupuncture-for-symptom-management-in-oncology-state-of-the-science-evidence-and-research-gaps
#3
Farah Z Zia, Oluwadamilola Olaku, Ting Bao, Ann Berger, Gary Deng, Arthur Yin Fan, Mary K Garcia, Patricia M Herman, Ted J Kaptchuk, Elena J Ladas, Helene M Langevin, Lixing Lao, Weidong Lu, Vitaly Napadow, Richard C Niemtzow, Andrew J Vickers, Xin Shelley Wang, Claudia M Witt, Jun J Mao
The Division of Cancer Treatment and Diagnosis, Office of Cancer Complementary and Alternative Medicine, at the National Cancer Institute (NCI) held a symposium on "Acupuncture for Cancer Symptom Management" on June 16 and 17, 2016. Invited speakers included 19 scientists and scholars with expertise in acupuncture and cancer research from the United States, Europe, and China. The conference reviewed the NCI's grant funding on acupuncture, analyzed the needs of cancer patients, reviewed safety issues, and assessed both the current scientific evidence and research gaps of acupuncture in oncology care...
November 1, 2017: Journal of the National Cancer Institute. Monographs
https://www.readbyqxmd.com/read/29137278/comprehensive-microrna-sequencing-of-exosomes-derived-from-head-and-neck-carcinoma-cells-in-vitro-reveals-common-secretion-profiles-and-potential-utility-as-salivary-biomarkers
#4
Scott Langevin, Damaris Kuhnell, Tess Parry, Jacek Biesiada, Shouxiong Huang, Trisha Wise-Draper, Keith Casper, Xiang Zhang, Mario Medvedovic, Susan Kasper
Exosomes are nano-scale, membrane encapsulated vesicles that are released by cells into the extracellular space and function as intercellular signaling vectors through horizontal transfer of biologic molecules, including microRNA (miRNA). There is evidence that cancer-derived exosomes enable the tumor to manipulate its microenvironment, thus contributing to the capacity of the tumor for immune evasion, growth, invasion, and metastatic spread. The objective of this study was to characterize differential secretion of exosomal miRNA by head and neck squamous cell carcinoma (HNSCC) and identify a set of candidate biomarkers that could be detected in non-invasive saliva samples...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29135257/field-theoretic-simulations-of-the-distribution-of-nanorods-in-diblock-copolymer-thin-films
#5
Huikuan Chao, Benjamin J Lindsay, Robert A Riggleman
Using block copolymer microphases to guide the self-assembly of nanorods in thin films can give rise to polymeric materials with unique optical, thermal and mechanical properties beyond those found in neat block copolymers. Often the design and manufacture of the materials require exquisite control of the nanorod distribution, which is experimentally challenging due to the large parameter space spanned by this class of materials. Simulation approaches, on the other hand, can access the thermodynamics that contribute to the nanorod distribution and hence offer valuable aide upon the design and manufacture of the materials...
November 14, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29101398/rotational-diffusion-of-soft-vesicles-filled-by-chiral-active-particles
#6
Jiamin Chen, Yunfeng Hua, Yangwei Jiang, Xiaolin Zhou, Linxi Zhang
We investigate the dynamics of two-dimensional soft vesicles filled with chiral active particles by employing the overdamped Langevin dynamics simulation. The unidirectional rotation is observed for soft vesicles, and the rotational angular velocity of vesicles depends mainly on the area fraction (ρ) and angular velocity (ω) of chiral active particles. There exists an optimal parameter for ω at which the rotational angular velocity of vesicle takes its maximal value. Meanwhile, at low concentration the continuity of curvature is destroyed seriously by chiral active particles, especially for large ω, and at high concentration the chiral active particles cover the vesicle almost uniformly...
November 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29099134/assessing-numerical-methods-for-molecular-and-particle-simulation
#7
Xiaocheng Shang, Martin Kröger, Benedict Leimkuhler
We discuss the design of state-of-the-art numerical methods for molecular dynamics, focusing on the demands of soft matter simulation, where the purposes include sampling and dynamics calculations both in and out of equilibrium. We discuss the characteristics of different algorithms, including their essential conservation properties, the convergence of averages, and the accuracy of numerical discretizations. Formulations of the equations of motion which are suited to both equilibrium and nonequilibrium simulation include Langevin dynamics, dissipative particle dynamics (DPD), and the more recently proposed "pairwise adaptive Langevin" (PAdL) method, which, like DPD but unlike Langevin dynamics, conserves momentum and better matches the relaxation rate of orientational degrees of freedom...
November 3, 2017: Soft Matter
https://www.readbyqxmd.com/read/29096482/fokker-planck-equation-for-the-non-markovian-brownian-motion-in-the-presence-of-a-magnetic-field
#8
Joydip Das, Shrabani Mondal, Bidhan Chandra Bag
In the present study, we have proposed the Fokker-Planck equation in a simple way for a Langevin equation of motion having ordinary derivative (OD), the Gaussian random force and a generalized frictional memory kernel. The equation may be associated with or without conservative force field from harmonic potential. We extend this method for a charged Brownian particle in the presence of a magnetic field. Thus, the present method is applicable for a Langevin equation of motion with OD, the Gaussian colored thermal noise and any kind of linear force field that may be conservative or not...
October 28, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29092424/the-underdamped-brownian-duet-and-stochastic-linear-irreversible-thermodynamics
#9
Karel Proesmans, Christian Van den Broeck
Building on our earlier work [Proesmans et al., Phys. Rev. X 6, 041010 (2016)], we introduce the underdamped Brownian duet as a prototype model of a dissipative system or of a work-to-work engine. Several recent advances from the theory of stochastic thermodynamics are illustrated with explicit analytic calculations and corresponding Langevin simulations. In particular, we discuss the Onsager-Casimir symmetry, the trade-off relations between power, efficiency and dissipation, and stochastic efficiency.
October 2017: Chaos
https://www.readbyqxmd.com/read/29089002/beyond-the-joint-the-role-of-central-nervous-system-reorganizations-in-chronic-musculoskeletal-disorders
#10
Jean-Sébastien Roy, Laurent J Bouyer, Pierre Langevin, Catherine Mercier
To a large extent, management of musculoskeletal disorders has traditionally focused on structural dysfunctions found within the musculoskeletal system, mainly around the affected joint. While a structural-dysfunction approach may be effective for musculoskeletal conditions in some populations, especially in acute presentations, its effectiveness remains limited in patients with recurrent or chronic musculoskeletal pain. Numerous studies have shown that the human central nervous system can undergo plastic reorganizations following musculoskeletal disorders; however, they can be maladaptive and contribute to altered joint control and chronic pain...
November 2017: Journal of Orthopaedic and Sports Physical Therapy
https://www.readbyqxmd.com/read/29079208/a-novel-biological-twin-father-temporal-paradox-of-general-relativity-in-a-g%C3%A3-del-universe-where-reproductive-biology-meets-theoretical-physics
#11
REVIEW
Hutan Ashrafian
Several temporal paradoxes exist in physics. These include General Relativity's grandfather and ontological paradoxes and Special Relativity's Langevin-Einstein twin-paradox. General relativity paradoxes can exist due to a Gödel universe that follows Gödel's closed timelike curves solution to Einstein's field equations. A novel biological temporal paradox of General Relativity is proposed based on reproductive biology's phenomenon of heteropaternal fecundation. Herein, dizygotic twins from two different fathers are the result of concomitant fertilization during one menstrual cycle...
October 25, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/29066966/signal-transmission-of-biological-reaction-diffusion-system-by-using-synchronization
#12
Lingli Zhou, Jianwei Shen
Molecular signal transmission in cell is very crucial for information exchange. How to understand its transmission mechanism has attracted many researchers. In this paper, we prove that signal transmission problem between neural tumor molecules and drug molecules can be achieved by synchronous control. To achieve our purpose, we derive the Fokker-Plank equation by using the Langevin equation and theory of random walk, this is a model which can express the concentration change of neural tumor molecules. Second, according to the biological character that vesicles in cell can be combined with cell membrane to release the cargo which plays a role of signal transmission, we preliminarily analyzed the mechanism of tumor-drug molecular interaction...
2017: Frontiers in Computational Neuroscience
https://www.readbyqxmd.com/read/29055335/transition-path-sampling-of-rare-events-by-shooting-from-the-top
#13
Hendrik Jung, Kei-Ichi Okazaki, Gerhard Hummer
Transition path sampling is a powerful tool in the study of rare events. Shooting trial trajectories from configurations along existing transition paths proved particularly efficient in the sampling of reactive trajectories. However, most shooting attempts tend not to result in transition paths, in particular in cases where the transition dynamics has diffusive character. To overcome the resulting efficiency problem, we developed an algorithm for "shooting from the top." We first define a shooting range through which all paths have to pass and then shoot off trial trajectories only from within this range...
October 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29055326/ab-initio-sampling-of-transition-paths-by-conditioned-langevin-dynamics
#14
Marc Delarue, Patrice Koehl, Henri Orland
We propose a novel stochastic method to generate Brownian paths conditioned to start at an initial point and end at a given final point during a fixed time tf under a given potential U(x). These paths are sampled with a probability given by the overdamped Langevin dynamics. We show that these paths can be exactly generated by a local stochastic partial differential equation. This equation cannot be solved in general but we present several approximations that are valid either in the low temperature regime or in the presence of barrier crossing...
October 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29053318/generic-properties-of-stochastic-entropy-production
#15
Simone Pigolotti, Izaak Neri, Édgar Roldán, Frank Jülicher
We derive an Itô stochastic differential equation for entropy production in nonequilibrium Langevin processes. Introducing a random-time transformation, entropy production obeys a one-dimensional drift-diffusion equation, independent of the underlying physical model. This transformation allows us to identify generic properties of entropy production. It also leads to an exact uncertainty equality relating the Fano factor of entropy production and the Fano factor of the random time, which we also generalize to non-steady-state conditions...
October 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29053287/general-criterion-for-harmonicity
#16
Karel Proesmans, Hans Vandebroek, Christian Van den Broeck
Inspired by Kubo-Anderson Markov processes, we introduce a new class of transfer matrices whose largest eigenvalue is determined by a simple explicit algebraic equation. Applications include the free energy calculation for various equilibrium systems and a general criterion for perfect harmonicity, i.e., a free energy that is exactly quadratic in the external field. As an illustration, we construct a "perfect spring," namely, a polymer with non-Gaussian, exponentially distributed subunits which, nevertheless, remains harmonic until it is fully stretched...
October 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29046990/active-force-maintains-the-stability-of-a-contractile-ring
#17
Stanard Mebwe Pachong, Kristian K Müller-Nedebock
We investigate a system of sufficiently dense polar actin filaments considered rigid and cross-linked by dimer myosin II protein within the contractile ring. The Langevin dynamics of this system is cast in a functional integral formalism and then transformed into density variables. Using the dynamical Random Phase Approximation (RPA) along with the a one-dimensional Langevin dynamics simulation (LDS), we investigate the structural integrity of the actin bundle network. The active force and the networking force reveal a non-trivial diffusive behaviour of the filaments within the ring...
October 23, 2017: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29045861/effects-of-nanopore-charge-decorations-on-the-translocation-dynamics-of-dna
#18
Ining Jou, Murugappan Muthukumar
We have investigated the dynamics of single-stranded DNA as it translocates through charge-mutated protein nanopores. Translocation of DNA is a crucial step in nanopore-based sequencing platforms, where control over translocation speed remains one of the main challenges. Taking advantage of the interactions between negatively charged DNA and positively charged amino acid residues, the translocation speed of DNA can be manipulated by deliberate charge decorations inside the nanopore. We employed coarse-grained Langevin dynamics simulations to monitor the step-by-step movement of DNA through different mutations of α-hemolysin protein nanopores...
October 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29038798/quantum-and-quasiclassical-trajectory-studies-of-rotational-relaxation-in-ar-n2-collisions
#19
Otoniel Denis-Alpizar, Oliver T Unke, Raymond J Bemish, Markus Meuwly
The collision of N2(+) with Ar is studied using quantum and classical methods. The dynamics was followed on a new potential energy surface based on ab initio energies computed at the UCCSD(T)-F12a/aug-cc-pVTZ level, using the correct analytical long range behaviour and a reproducing kernel representation. Comparison with multi-reference MRCI+Q calculations establish that UCCSD(T)-F12a is a sufficiently high level of theory for this problem. Results from quantum close coupling and quasiclassical trajectory calculations agree favourably with each other and the rates for inelastic collisions are lower than those from Langevin theory...
October 25, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29038251/stress-introduction-rate-alters-benefit-of-acrab-tolc-efflux-pumps
#20
Ariel M Langevin, Mary J Dunlop
Stress tolerance studies are typically conducted in an all-or-none fashion. However, in realistic settings-such as in clinical or metabolic engineering applications-cells may encounter stresses at different rates. As such, how cells tolerate stress may depend on its rate of appearance. To address this, we study how the rate of introduction affects bacterial stress tolerance by focusing on a key mechanism for stress response. Efflux pumps, such as AcrAB-TolC from Escherichia coli, are membrane transporters well known for their ability to export a wide variety of substrates, including antibiotics, signaling molecules, and biofuels...
October 16, 2017: Journal of Bacteriology
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