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Monticelli Luca - - 2013
In this chapter we review the basic features and the principles underlying molecular mechanics force fields commonly used in molecular modeling of biological macromolecules. We start by summarizing the historical background and then describe classical pairwise additive potential energy functions. We introduce the problem of the calculation of nonbonded interactions, ...
Noid W G - - 2013
This chapter provides a primer on theories for coarse-grained (CG) modeling and, in particular, reviews several systematic methods for determining effective potentials for CG models. The chapter first reviews a statistical mechanics framework for relating atomistic and CG models. This framework naturally leads to a quantitative criterion for CG models ...
Lu Zhong-Yuan - - 2013
Dissipative particle dynamics (DPD) is a particle-based mesoscopic simulation method, which facilitates the studies of thermodynamic and dynamic properties of soft matter systems at physically interesting length and time scales. In this method, molecule groups are clustered into the dissipative beads, and this coarse-graining procedure is a very important aspect ...
Cisneros G Andrés - - 2013
Electrostatic interactions are crucial for both the accuracy and performance of atomistic biomolecular simulations. In this chapter we review well-established methods and current developments aiming at efficiency and accuracy. Specifically, we review the classical Ewald summations, particle-particle particle-method particle-method Ewald algorithms, multigrid, fast multipole, and local methods. We also highlight ...
Laasonen Kari - - 2013
In this chapter, an introduction to ab initio molecular dynamics (AIMD) has been given. Many of the basic concepts, like the Hellman-Feynman forces, the difference between the Car-Parrinello molecular dynamics and AIMD, have been explained. Also a very versatile AIMD code, the CP2K, has been introduced. On the application, the ...
Baoukina Svetlana - - 2013
A lipid monolayer lining a boundary between two immiscible phases forms a complex interface with inhomogeneous distribution of forces. Unlike lipid bilayers, monolayers are formed in asymmetric environment and their properties depend strongly on lipid surface density. The monolayer properties are also affected significantly by the representation of the pure ...
Sapay Nicolas - - 2013
Modeling of carbohydrates is particularly challenging because of the variety of structures resulting for the high number of monosaccharides and possible linkages and also because of their intrinsic flexibility. The development of carbohydrate parameters for molecular modeling is still an active field. Nowadays, main carbohydrates force fields are GLYCAM06, CHARMM36, ...
Steinbrecher Thomas - - 2013
Molecular dynamics simulations of biomolecules have matured into powerful tools of structural biology. In addition to the commonly used empirical force field potentials, quantum mechanical descriptions are gaining popularity for structure optimization and dynamic simulations of peptides and proteins. In this chapter, we introduce methodological developments such as the QM/MM ...
Lodola Alessio - - 2013
Techniques for modelling enzyme-catalyzed reaction mechanisms are making increasingly important contributions to biochemistry. They can address fundamental questions in enzyme catalysis and have the potential to contribute to practical applications such as drug development.
Enkavi Giray - - 2013
Membrane transporters facilitate active transport of their specific substrates, often against their electrochemical gradients across the membrane, through coupling the process to various sources of cellular energy, for example, ATP binding and hydrolysis in primary transporters, and pre-established electrochemical gradient of molecular species other than the substrate in the case ...
Periole Xavier - - 2013
The Martini force field is a coarse-grained force field suited for molecular dynamics simulations of biomolecular systems. The force field has been parameterized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. In this chapter ...
Khalid Syma - - 2013
The time and length scales accessible by biomolecular simulations continue to increase. This is in part due to improvements in algorithms and computing performance, but is also the result of the emergence of coarse-grained (CG) potentials, which complement and extend the information obtainable from fully detailed models. CG methods have ...
Derreumaux Philippe - - 2013
Coarse-grained models for protein folding and aggregation are used to explore large dimension scales and timescales that are inaccessible to all-atom models in explicit aqueous solution. Combined with enhanced configuration search methods, these simplified models with various levels of granularity offer the possibility to determine equilibrium structures, compare folding kinetics ...
Groenhof Gerrit - - 2013
Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have become a popular tool for investigating chemical reactions in condensed phases. In QM/MM methods, the region of the system in which the chemical process takes place is treated at an appropriate level of quantum chemistry theory, while the remainder is described by a ...
Bortolato Andrea - - 2013
Molecular docking represents an important technology for structure-based drug design. Docking is a computational technique aimed at the prediction of the most favorable ligand-target spatial configuration and an estimate of the corresponding complex free energy, although as stated at the beginning accurate scoring methods remain still elusive. In this chapter, ...
Foloppe Nicolas - - 2013
The structure and dynamics of the B-DNA double helix involves subtle sequence-dependent effects which are decisive for its function, but difficult to characterize. These structural and dynamic effects can be addressed by simulations of DNA sequences in explicit solvent. Here, we present and discuss the state-of-art of B-DNA molecular dynamics ...
Moradi Mahmoud - - 2013
During the last decade, several methods for sampling phase space and calculating various free energies in biomolecular systems have been devised or refined for molecular dynamics (MD) simulations. Thus, state-of-the-art methodology and the ever increasing computer power allow calculations that were forbidden a decade ago. These calculations, however, are not ...
Martinez-Seara Hector - - 2013
Simulations based on molecular dynamics (MD) are an important tool in structural biology. In the field of lipid membrane research, MD represents a major tool as it grant access to atomic level features of the membrane difficult to access by experimental means. In this chapter we describe step by step ...
Antila Hanne S - - 2013
This chapter provides an overview of the most common methods for including an explicit description of electronic polarization in molecular mechanics force fields: the induced point dipole, shell, and fluctuating charge models. The importance of including polarization effects in biomolecular simulations is discussed, and some of the most important achievements ...
Johansson Mikael P - - 2013
This chapter introduces the theory and applications of commonly used methods of electronic structure calculation, with particular emphasis on methods applicable for modelling biomolecular systems. This chapter is sectioned as follows. We start by presenting ab initio methods, followed by a treatment of density functional theory (DFT) and some recent ...
Hug Susanna - - 2013
This chapter provides an overview of the various techniques that are commonly used in classical molecular dynamics simulations. It describes suitable algorithms for the integration of Newton's equation of motion over many time steps for systems containing a large number of particles, different choices of boundary conditions as well as ...
Shirts Michael R - - 2013
Free energy calculations are extremely useful for investigating small-molecule biophysical properties such as protein-ligand binding affinities and partition coefficients. However, these calculations are also notoriously difficult to implement correctly. In this chapter, we review standard methods for computing free energy via simulation, discussing current best practices and examining potential pitfalls ...
Mitsutake Ayori - - 2013
In biomolecular systems (especially all-atom models) with many degrees of freedom such as proteins and nucleic acids, there exist an astronomically large number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in states of these energy local minima. Enhanced ...
Sanejouand Yves-Henri - - 2013
Fifteen years ago, Monique Tirion showed that the low-frequency normal modes of a protein are not significantly altered when nonbonded interactions are replaced by Hookean springs, for all atom pairs whose distance is smaller than a given cutoff value. Since then, it has been shown that coarse-grained versions of Tirion's ...
Praprotnik Matej - - 2013
We review the basic theoretical principles of the adaptive resolution simulation scheme (AdResS). This method allows to change molecular resolution on-the-fly during a simulation by changing the number of degrees of freedom in specific regions of space where the required resolution is higher than in the rest of the system. ...
Shillcock Julian C - - 2013
Biological cells are highly dynamic, and continually move material around their own volume and between their interior and exterior. Much of this transport encapsulates the material inside phospholipid vesicles that shuttle to and from, fusing with, and budding from, other membranes. A feature of vesicles that is crucial for this ...
Basheer Khadijah K Central Middlesex Hospital, Acton Lane, Park Royal, London, NW10 7NS, United Kingdom. - - 2013
We present the case of a 59-year-old woman whose silicone punctal plugs migrated distally causing lacrimal obstruction. The plugs were removed from the lacrimal sac during endoscopic endonasal dacrocystorhinostomy and is illustrated by endoscopic photographs and videos taken at the time of surgery. This case highlights the potential complications of ...
Chak Garrick G Gavin Herbert Eye Institute, University of California, Irvine, CA 92697-4375, USA. - - 2013
The aim of this article was to describe positive sentinel lymph node biopsy (SLNB) findings in patients with periocular invasive squamous cell carcinoma (SCC). This was a retrospective chart review of 5 patients with invasive SCC of the periocular region who underwent SLNB and were found to have regional metastasis. ...
Rabinowitz Michael P MP Oculoplastic and Orbital Surgery Service, Wills Eye Institute, Philadelphia, PA 19107, USA. - - 2013
A 48-year-old man was seen in the Wills Eye Institute emergency room for pain and decreased vision after having a diesel engine fuel cylinder explosion in his face. Clinical examination showed proptosis, decreased extraocular motility, and increased intraocular pressure; CT scan imaging revealed hypodense areas within the orbit. His orbital ...
Walsh Ryan D RD Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA. - - 2013
Adenoid cystic carcinoma is an uncommon malignant tumor of epithelial origin typically arising from salivary glands. Orbital involvement may occur via direct or perineural spread from a lacrimal gland or sinonasal source. Primary orbital adenoid cystic carcinoma without involvement of the lacrimal gland is rare. The authors report a 53-year-old ...
Carruth Bryant P BP Division of Ophthalmic Plastic Surgery, Lions Eye Institute, Department of Ophthalmology, Albany Medical Center, Albany, New York, USA. - - 2013
To describe and evaluate a modified technique for blepharoptosis repair via Müller's muscle-conjunctival resection. An observational case series is reported. Records of 29 consecutive patients (42 eyelids) with blepharoptosis undergoing internal ptosis repair between January 2008 and December 2010 were reviewed including detailed preoperative and postoperative evaluations, eyelid measurements, surgical ...
DeCarli Charles C Alzheimer's Disease Center, Imaging of Dementia and Aging (IDeA) Laboratory, Department of Neurology and Center for Neuroscience, University of California at Davis, CA 95817, USA. - - 2013
Cerebrovascular risk factors and stroke are highly prevalent with advancing age, and stroke may be more common than Alzheimer's disease, particularly among older men. While stroke mortality continues to decline, the prevalence of individuals with various vascular risk factors continues to rise and many are undiagnosed or undertreated. Asymptomatic cerebrovascular ...
Neelov I M IM Department of Chemistry, University of Helsinki, FIN00014, A.I.Virtasen Aukio 1, Helsinki, - - 2013
Prevention of amyloidosis by chemical compounds is a potential therapeutic strategy in Alzheimer's, prion and other neurodegenerative diseases. Regularly branched dendrimers and less regular hyperbranched polymers have been suggested as promising inhibitors of amyloid aggregation. As demonstrated in our previous studies, some widely used dendrimers (PAMAM, PPI) could not only ...
Bhatnagar Parijat P Baylor College of Medicine & Texas Children's Hospital, Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, Houston, TX 77030, - - 2013
Adoptive transfer of primary T cells genetically modified to have desired specificity can exert an anti-tumor response in some patients. To improve our understanding of their therapeutic potential we have developed a clinically-appealing approach to reveal their in vivo biodistribution using nanoparticles that serve as a radiotracer for imaging by ...
Westmark Cara J CJ Waisman Center for Developmental Disabilities, University of Wisconsin, Madison, WI 53705, USA. - - 2013
Seizures are a common phenotype in many neurological disorders including Alzheimer's disease, Down syndrome, and fragile X syndrome. Mouse models of these disorders overexpress amyloid-β protein precursor (AβPP) and amyloid-β (Aβ) and are highly susceptible to audiogenic-induced seizures (AGS). We observed decreased AGS in these mice fed a casein-based, purified ...
Ozair Mohammad Zeeshan MZ Laboratory of Molecular Embryology, The Rockefeller University, New York, New York 10065, - - 2013
Human embryonic stem cells (hESCs) provide a valuable window into the dissection of the molecular circuitry underlying the early formation of the human forebrain. However, dissection of signaling events in forebrain development using current protocols is complicated by non-neural contamination and fluctuation of extrinsic influences. Here, we show that SMAD7, ...
Lindsley William G - - 2012
Few studies have quantified the dispersion of potentially infectious bioaerosols produced by patients in the health care environment and the exposure of health care workers to these particles. Controlled studies are needed to assess the spread of bioaerosols and the efficacy of different types of respiratory personal protective equipment (PPE) ...
Murray Patrick R PR Becton Dickinson Diagnostic Systems, Sparks, MD, - - 2012
Healthcare systems spend considerable resources collecting and processing blood cultures for the detection of blood stream pathogens. The process is initiated with the collection of blood cultures that depend upon proper skin disinfection, collection of an adequate number of specimens and volume of blood, and prompt processing in a sensitive ...
Ceyhan Elvan E Department of Mathematics, College of Sciences, Koç University, Istanbul, - - 2012
Manipulation and encapsulation of cells in microdroplets has found many applications in various fields such as clinical diagnostics, pharmaceutical research, and regenerative medicine. The control over the number of cells in individual droplets is important especially for microfluidic and bioprinting applications. There is a growing need for modeling approaches that ...
Shi Yanxiang Y Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, - - 2012
We report the heterologous production of Ala(0)actagardine in E. coli by co-expression of the substrate peptide GarA and its modification enzymes GarM and GarO. The activity of GarO, a luciferase-like monooxygenase that introduces the unique sulfoxide group of actagardine, was also investigated in vitro.
Grivennikov Sergei I SI Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California 92093-0723, - - 2012
Approximately 2% of colorectal cancer is linked to pre-existing inflammation known as colitis-associated cancer, but most develops in patients without underlying inflammatory bowel disease. Colorectal cancer often follows a genetic pathway whereby loss of the adenomatous polyposis coli (APC) tumour suppressor and activation of β-catenin are followed by mutations in ...
Richards Ayo-Lynn - - 2012
The aim of this article is to describe complications of hydrogel (MIRAgel) scleral buckle implants that may appear many years after implantation, and to describe an effective technique to facilitate safe removal of these implants, which become extremely friable with time. Four case reports of patients with complications of hydrogel ...
Elmann Solly - - 2012
The aim of this article was to report the clinical presentation, radiography, culture results, treatment modalities, and outcomes of periocular abscesses associated with brow epilation. This was a retrospective case series including 26 patients referred for periocular abscess following brow epilation. Twenty-six female patients with a median age of 20.5 ...
Park Juwan - - 2012
To examine the relative positions of the lacrimal fossa (LF) and the bony nasolacrimal canal (BNLC) in relation to each other and a reference plane. Forty-two orbits and BNLCs from 21 Asian cadavers (9 men and 12 women; average age at death, 84.4 years; range, 70-99 years) had been fixed ...
Aakalu Vinay - - 2012
To determine whether the Putterman-Gladstone tube is a safe and effective lacrimal bypass tube in conjunctival dacryocystorhinostomy surgery. The authors retrospectively reviewed the charts of patients who underwent conjunctival dacryocystorhinostomy with the Putterman-Gladstone tube between January 1994 and December 2010. Clinical data reviewed included demographics, ocular and surgical history, epiphora ...
Fezza John P - - 2012
A youthful female upper eyelid contour includes a concave medial portion of the upper eyelid along with a fuller, convex lateral eyelid. The skin in the lateral eyelid is tight without hooding. This is a sigmoid shape in 3-dimensional terms. With aging, fatty herniation medially along with redundant, hooded, ptotic ...
Powell Suzanne K - - 2012
When someone is very ill or has lost a loved one, this may be the hardest time to say the right words. Guidance is given on communication during these times.
Glendenning-Napoli Alison - - 2012
PURPOSE OF THE STUDY:: To examine the effects of a community-based case management program on acute health care utilization and associated costs in uninsured patients with 1 or more chronic diseases. PRIMARY PRACTICE SETTING:: Large regional academic medical center that provides health care services for the vast majority of indigent ...
Lee Brian J - - 2012
To determine surgical outcomes after external dacryocystorhinostomy (DCR) surgery in patients with Wegener granulomatosis (WG). The authors retrospectively reviewed the charts of consecutive patients with WG who underwent primary or secondary external DCR surgery between January 2001 and January 2010. Clinical data reviewed included patient demographics, systemic disease involvement and ...
Cohen Daniel H - - 2012
To evaluate methods of logic, set theory, and information theory in developing a conceptual framework that would be useful in an educational process as well as in developing a consistent and rational method for hospital status determination. To implement these methods on a daily basis in interaction with nurse case ...
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