Hiqmet Kamberaj

National Institute of Physics

We used adaptive umbrella sampling on a modified version of the roll angle to simulate the bending of DNA dodecamers. Simulations were carried out with the AMBER and CHARMM force fields for 10 sequences in which the central base pair step was varied. On long length scales, the DNA behavior was found to be consistent with the worm-like chain model....

The information theory measure of transfer entropy is used to extract the causality of correlated motions from molecular dynamics simulations. For each pair of correlated residues, the method quantifies which residue drives the correlated motions, and which residue responds. The measure reveals how correlated motions are used to transmit informatio...

Molecular dynamics integrators are presented for translational and rotational motion of rigid molecules in microcanonical, canonical, and isothermal-isobaric ensembles. The integrators are all time reversible and are also, in some approaches, symplectic for the microcanonical ensembles. They are developed utilizing the quaternion representation on...

This chapter introduces the superposition of waves. It discusses the interference phenomena, standing waves, and beats.

The learning outcomes are different for the courses taught at the physics undergraduate programs at the university level because of the prerequisites. Besides, determining the electrostatic potential is part of the physics curricula taught at the university's undergraduate or graduate physics degrees. The concept is necessary for a high level of ma...

Sound waves are the most critical example of longitudinal waves. They can travel through any material medium with a speed that depends on the properties of the medium. As the waves travel, the particles in the medium vibrate to produce changes in density and pressure along the direction of motion of the wave. These changes result in a series of hig...

The chapter aims to introduce the mechanical waves.

In this paper, we focus on the influence of Riemann space-time curvature on the laws of electro-magnetism, such as Gauss's law, Maxwell-Ampére's law, and Faraday's law. Furthermore, we also introduce the work done on the unification of the gravitation and electromagnetic fields.

In this paper, we will describe the general theory of relativity. The special theory of relativity is based on the ideal inertial frames. These ideal inertial frames are assumed to exist in every event in space-time. In contrast, in the general theory of relativity, we do not have to make that assumption. Additionally, the space-time is considered...

In this paper, we will describe the energy-momentum density tensor of the matter. The main focus is on the discussion of the conservation laws of the general theory of relativity.

Using a notably large amount of data in investigating physical and chemical phenomena demands new statistical and computational approaches; besides, the cross-validations require well established theoretical frameworks. This study aims to validate the statistical efficiency of alternative definitions for the information-theoretic measures, such as...

This paper gives an introduction to relativistic electromagnetism. First, we start showing the invariance form of Maxwell's equations, which implies the covariance of electromagnetism. Then, we present the Lorentz transformations of the electromagnetic field vectors. In addition, we describe in detail the dynamics of a relativistic charged particle...

This study will continue the scientific research in physics and chemistry, particularly in using theoretical and computational methods such as molecular dynamics methods at the classical and ab-initio levels for the molecular and atomic systems. The necessary efforts have been seen in recent years to replace the traditional solvents, which are che...

Galilean transformations and Lorentz transformations are part of the curricula in modern physics at the upper-secondary schools (such as Grade 11, 12, or Grade 13) and in physics undergraduate programs at any university. However, learning outcomes are different for these courses taught at the upper-secondary schools and physics undergraduate progra...

Includes comprehensive summary of quantum mechanical molecular dynamics and computational techniques related to it Provides pedagogical tutorials and sample algorithms for performing simulations and analyzing the data Targets broad range of fields from biophysics to material science Part of the book series: Scientific Computation (SCIENTCOMP)

This chapter introduces the normal mode analysis of a protein, which is associated with the energy minimisation.

This chapter introduces the setup protocol for preparing a molecular biological system simulation in explicit solvent. The energy minimisation methods are discussed in details. Furthermore, the complete protocol of the equilibration of solvent is shown for a protein system in explicit solvent.

This chapter describes how to run standard MD simulations of a biological system in explicit solvent using different statistical ensembles and numerical integrators.

In this chapter, we introduce the quantum mechanics molecular models and quantum mechanics molecular dynamics simulations of molecules and biomolecular systems. Besides, the numerical aspects of the non-relativistic electronic structure of molecular systems will be discussed.

In this chapter, we discuss the basis set functions for standard molecular quantum mechanics calculations. Furthermore, the basis sets for quantum periodic systems, such as solids and metals, will be described.

This chapter describes the principal components analysis of biological systems in explicit solvent and the stability of the principal components analysis by comparing the quasi-harmonic modes of different simulation trajectories of the same system.

In this chapter, we discuss the computational molecular modelling strategies. In particular, the CHARMM molecular mechanics force field of biomolecules is introduced and its parametrisation. For more information about other molecular mechanics force fields and molecular modelling strategies, one can consider the following literature (Leach 2001). B...

In this chapter, we will briefly describe a Python interactive graphical user interface (GUI) for CHARMM package for performing MD simulations of a biological molecular system and standard analysis of in silico data produced from the simulations.

In this chapter, the computational coarse-grain modelling strategies are discussed. Besides, different coarse-grained models (CGMs) will be described.

Molecular dynamics simulations at atomic level have widely been used in studying macromolecular systems, such as protein, DNA and their complexes, mainly because the laws of classical statistical mechanics can largely govern the processes involved at the experimental conditions. Macromolecules, such as proteins, are characterised by dynamics with t...

In this chapter, we will briefly describe the practical aspects of molecular dynamics simulations, such as designing the constraints, periodic boundary conditions, spherical cutoffs, treatment of the long-range interactions (in particular, electrostatic interactions), and identifying the equilibrium states of the simulations.

In this chapter, we focus on the semi-empirical quantum mechanics approaches and their use in computer simulations.

This chapter introduces the machine learning quantum mechanics methods and their use in computer simulations. In particular, the focus is on the use of machine learning approach in predicting the potential electronic energy surface and its gradient for QM molecular dynamics simulations.

The 21st century is the Information Age, characterised by an economy based on information computerisation. In this new era of computing, the role of physics is becoming crucial and practical. Thus, physics is not seen anymore as an abstract and purely academic endeavour. This study addresses physics inventions' contributions to computer science, so...

This book covers the lecture notes of the course ``Introduction to Algorithms" for the Computer Engineering students.

Cephalometric analysis is very essential for the patient having dentofacial and craniofacial deformities. The manual localization of the cephalometric landmarks is also important and critical for the observer that is required to be performed by the orthodontics only. The manual localization is the time consuming and the tedious task for the observe...

In this chapter, we will introduce capacitance and dielectrics. Then, we discuss the electrostatics of macroscopic media and introduce a molecular theory of dielectrics. Also, we will introduce electric polarization, and then derive Maxwell’s equations for an electrostatic field in both free space and dielectric media. As extra reading material, th...

In this chapter, we will introduce electrostatic potential and discuss the methods used to calculate the electrostatic potential. Furthermore, we present the potential difference and equipotential surfaces. Moreover, we will discuss the calculation of the electrostatic potential for a single-point charge and system of charges. As extra reading mate...

In this study, two approaches were applied to enhance the conformational search from molecular dynamics simulations to determine the transition states of a potential energy surface topology. The main focus is on the augmented dynamics using the swarm particle intelligence and Tsallis statistics molecular dynamics simulations of the phase transition...

In this chapter, we introduce magnetism in the matter. We first discuss the magnetic moments of an atom of matter. Then, we will discuss the magnetic substances, such as ferromagnetic, paramagnetic, and diamagnetic substances. Next, we will introduce Faraday’s law of induction. Finally, we will introduce the famous Maxwell equations of electromagne...

In this chapter, we discuss the applications of electromagnetic theory to electrostatic properties of macromolecular solutions and wireless charging. For further reading, one can also consider other available literature Kamberaj (2020); Deuflhard et al. (1997).

In this chapter, we introduce some more information about Faraday’s law of induction. For further reading, one can also consider other available literature Holliday et al. (2011).

In this chapter, we introduce the sources of the magnetic field. In particular, we introduce Biot-Savart law and the magnetic forces between the current-carrying parallel conductors. Also, we introduce Ampére’s law and the magnetic field flux. Then, Gauss’s law and Maxwell-Ampére’s law will be presented. As extra reading material, the reader can al...

In this chapter, we discuss the electromagnetic wave equations in vacuum and linear media. Furthermore, the reflection’s law and the Snell’s law are derived, along with the polarization of electromagnetic planar waves and Fresnel’s equations.

In this chapter, we discuss Maxwell’s equations of electromagnetism. Magnetic and electrostatic fields exist together, and hence it makes sense to always discuss the two fields simultaneously under electromagnetism. That is, often, the electromagnetism is represented by electromagnetic field, which is the pair of vectors \((\mathbf {E},\mathbf {B})...

In this chapter, we will introduce the electric current. We introduced charges at rest, or electrostatics, so far. In this chapter, we will consider the phenomena associated with electric charges in motion. We will introduce the electric current, or simply current, which describes the rate of charge flow through some region of space. Also, in this...

In this chapter, we will introduce the magnetic field. We described the interactions between charged objects in terms of electric fields. An electric field associates with any stationary or moving electric charge. In addition to an electric field, the region of space surrounding any moving electric charge also contains a magnetic field. A magnetic...

In this chapter, we introduce the electric flux and Gauss’s law. Also, the application of Gauss’s law to insulators and conductors will be discussed. As extra reading material, the reader can also consider other literature (Holliday et al. 2011). The electric flux concept describes quantitatively the electric lines. The number of field lines per un...

In this chapter, we will introduce the electrostatics in free space. First, we will introduce the concept of the charges, and then present Coulomb’s law of the interactions between the charges. Next, we discuss the concept of electric field and electric field lines. Also, we will describe the motion of a charged particle in the presence of an elect...

In this chapter, we derive electromagnetic wave equations in dispersive media. This chapter describes the absorption, Lorentz’s oscillator model of a dielectric, the wave equation of a conductor, the wave equation of a dilute plasma, and the magnetized plasma or dielectric.

Fog computing (FC) models the cloud computing paradigm expedient by bridging the breach between centralized data servers and diverse terrestrially distributed applications. It wields various wireless sensor networks (WSNs) that sprawl in the core of any IoT applications. Consequently, the operation of fog network turns on the efficiency of WSNs ope...

In this study, we employed a newly developed method to predict macromolecular properties using a swarm artificial neural network (ANN) method as a machine learning approach. In this method, the molecular structures are represented by the feature description vectors used as training input data for a neural network. This study aims to develop an effi...

Theileria and Babesia species are eukaryotic protozoan parasites classified under the order Piroplasmida of the phylum Apicomplexa. Tick vectors transmit these microorganisms in tropical and subtropical regions to a wide range of animals, including ruminants, causing fatal and life-threatening diseases such as bovine babesiosis and theileriosis. Re...

Artificial Intelligence (AI) has an impressively wide range of capabilities, such as making decisions in real-time based on computing technologies and various predefined algorithms. The departments of Human Resources Management (HRM) will also experience the impact of AI. For a smooth workflow and intuitive work environment, HRM professionals under...

This textbook covers all fundamental concepts of physics and describes how different theories are developed from physical observations and phenomena. After some essential calculus the author presents the complete classical mechanics giving numerous examples and with a clear focus on problem-solving techniques. Due to the high number of exercises a...

This study combines the information- and graph-theoretic measures to investigate the cluster modulation of the amino acid residues and nucleotides at complex biomolecular interfaces. The symbolic transfer entropy is used as an information-theoretic measure. I also used graph theory to obtain information and heat flow weighted digraph models used to...

This chapter aims to discuss different methods used to determine the frequency spectrum of the motions in a macromolecular system, namely the normal modes, principal components analysis, and the time-lagged auto-encoder machine learning approach.

In this chapter, we will discuss numerical integrator algorithms used for solving differential equations used in molecular dynamics simulations. In particular, we will propose different numerical integrator algorithms, which satisfy time reversibility or symplectic properties.

Many interesting problems that we would like to treat using computational molecular modeling are unfortunately too large to be considered by quantum mechanics (QM). Quantum mechanics methods consider the electronic structure in a molecular system. Even when some of the electrons are omitted, still a large number of particles must be considered, whi...

In this chapter, we will discuss some of the elements of the information theory measures. In particular, we will introduce the so-called Shannon and relative entropy of a discrete random process and Markov process. Then, we will discuss the relationship between the entropy using the thermodynamic view and information theory view.

Generalized ensemble molecular dynamics simulation methods can be used to improve the sampling of lower energy configurations.

In this chapter, we will present the most advanced methods used in the calculation of free energy from the computer simulations. First, in this chapter, we will discuss the methods employed in molecular dynamics simulations using explicit solvent models, such as the thermodynamic free energy perturbation method, thermodynamic integration method, an...

In this chapter, we will present some important concepts of classical mechanics.

Molecular dynamics simulations at atomic level have widely been used in studying macromolecular systems, such as protein, DNA and their complexes, mainly because the laws of classical statistical mechanics can largely govern the processes involved at the experimental conditions. Macromolecules, such as proteins, are characterized by dynamics with t...

In this chapter, we will introduce some practical aspects of molecular dynamics simulations, such as designing the constraints (e.g., SHAKE), periodic boundary conditions, spherical cutoffs, treatment of the long-range interactions (in particular, electrostatic interactions), and identifying the equilibrium states of the simulations.

This book presents computer simulations using molecular dynamics techniques in statistical physics, with a focus on macromolecular systems. The numerical methods are introduced in the form of computer algorithms and can be implemented in computers using any desired computer programming language, such as Fortran 90, C/C++, and others. The book also...

Symbolic Information Flow Measurement software is used to compute the information flow between different components of a dynamical system or different dynamical systems using symbolic transfer entropy. The time series represents the time evolution trajectory of a dynamical system. We introduce a method to perform a symbolic analysis of the time ser...

To provide accurate predictions of different thermodynamic properties of the (bio)molecular systems, such as free energy of hydration, pKa, binding energy, or quantum mechanical properties, is challenging and computationally time-consuming. Besides, the consistency among all other molecular systems already optimized remains still challenging and pe...

In this study, we employed a novel method for prediction of (macro)molecular properties using a swarm artificial neural network method as a machine learning approach. In this method, a (macro)molecular structure is represented by a so-called description vector , which then is the input in a so-called bootstrapping swarm artificial neural network (B...

This book presents some solved problems on Physics I, which covers the materials of the lecture notes for Physics I course for Science and Engineering students.

This book covers the lecture notes of General Physics delivered for students of Biology.

This book contains a set of lectures notes delivered for the students of the engineering. It can also be used for the students of science.

Molecular dynamics (MD) simulations at atomic level have widely been used in studying macromolecular systems, such as protein, DNA and their complexes, mainly because the classical statistical mechanic's laws can explain different phenomena occurring at specified experimental conditions. In this study, we will present the most advanced methods used...

Computer simulations are used very often to understand and solve practical problems in the area of statistical physics and biophysics. With proper knowledge of Classical Mechanics, Thermodynamics and Statistical Physics, you will be able to understand and judge the content of this book. This book aims to be a recipe for computer simulations with m...

# sifm Symbolic Information Flow Measurement: Transfer Entropy, Local Transfer Entropy and Mutual Information #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # Id: Readme.txt,v 1.0 19-03-2018, IBU # # This source code is part of # # Symbolic Information Flow Measure Code for styding the...

Replica Exchange Using Swarm Particle-like Molecular Dynamics This is a C++ computer program for performing Replica Exchange Standard and/or Swarm Particle-like Molecular Dynamics Simulations of (bio)molecular systems using Coarse-graining models for proteins. The coarse-graining model includes these terms: 1 - Electrostatic interactions by assign...

# bsann Bootstrapping Swarm Neural Network # Bootstrapping Swarm Artificial Neural Network Program # # VERSION 1.0 # # Written by Hiqmet Kamberaj. # Copyright (C) 2018 Hiqmet Kamberaj. # Check out h.kamberaj@gmail.com for more information. # # This program is free software; you can redistribute it and/or modify it under # the terms of the GNU Ge...

Symbolic Information Flow Measurement software is used to compute the information flow between different components of a dynamical system using symbolic transfer entropy. Here, the time series represents time evolution trajectory of a component of the dynamical system. Different methods are used to perform symbolic analysis of the time series based...

In this study, we compared the contributions of polar and nonpolar interactions to the solvation free energy of a solute in solvent, which is decomposed into four different terms based on the nature of interactions: (i) electrostatic solvation free energy term counting for the work done to move solute charges from fixed points in some reference env...

In this paper, we studied the efficiency of defining the subspace of the slow protein motion for describing long time scale dynamics. To address the problem of the correlations between the slow and the fast modes, we investigated the separation of time scales provided by the Principal Component Analysis (PCA) method. In our study, two systems have...

In the chapter we discuss the principles of the classical thermodynamics. In particular we will describe the laws of thermodynamics, thermodynamic functions, Maxwell relations, and stability of thermodynamical systems.

In this chapter we will review some basic concepts of thermodynamics and statistical mechanics. Furthermore, we will discuss the energy and/or particle number fluctuations in different statistical ensembles and their differences. 3.1 Systems In statistical mechanics systems play the same role as particles in kinetic theory. The system has a very ge...

This chapter aims to discuss the application of the statistical mechanics (or the so-called statistical thermodynamics) in understanding biological phenomena, based on the theoretical framework introduced by Lazaridis and Karplus (2003).

In this chapter we will discuss advanced methods used in molecular dynamics simulation in order to improve the efficiency of technique. 10.1 Introduction Atomistic molecular dynamics (MD) method now plays a major role in studying macromolecular systems [214], this due to, in part, the fact that processes involved at the experimental conditions can...

We present a newly developed Replica Exchange algorithm using q -Gaussian Swarm Quantum Particle Optimization (REX@q-GSQPO) method for solving the problem of finding the global optimum. The basis of the algorithm is to run multiple copies of independent swarms at different values of q parameter. Based on an energy criterion, chosen to satisfy the d...

In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a c...

Protozoan parasites of the genera Trypanosoma and Leishmania are causative agent of tropical diseases known as trypanosomiasis and leishmaniasis. They kill hundreds of thousands and affect about 30 million of people and life stocks1,2. Trypanosomatids have unique dithiol trypanothione dependent oxidant detoxification mechanism which is absent in ma...

We present a newly developed Replica Exchange algorithm using q -Gaussian Swarm Quantum Particle Optimization (REX@q-GSQPO) method for solving the problem of finding the global optimum. The basis of the algorithm is to run multiple copies of independent swarms at different values of q parameter. Based on an energy criterion, chosen to satisfy the d...

A coarse grained model in the frame work of principal component analysis is presented. We used a bath of harmonic oscillators approach, based on classical mechanics, to derive the generalized Langevin equations of motion for the collective coordinates. The dynamics of the protein collective coordinates derived from molecular dynamics simulations ha...