Introduction: In tissue engineering, the interaction among three primary elements, namely cells, material scaffolds, and stimuli, plays a pivotal role in determining the fate of cells and the formation of new tissue. Understanding the characteristics of these components and their interplay through various methodologies can significantly enhance the efficiency of the designed tissue engineering system. In silico methods, such as molecular dynamics (MD) simulation, use mathematical calculations to investigate molecular properties and can overcome the limitations of laboratory methods in delivering adequate molecular-level information. Methods: The studies that used molecular dynamics simulation, either alone or in combination with other techniques, have been reviewed in this paper. Results: The review explores the use of molecular dynamics simulations in studying substrate formation mechanism and its optimization. It highlights MD simulations' role in predicting biomolecule binding strength, understanding substrate properties' impact on biological activity, and factors influencing cell attachment and proliferation. Despite limited studies, MD simulations are considered a reliable tool for identifying ideal substrates for cell proliferation. The review also touches on MD simulations' contribution to cell differentiation studies, emphasizing their role in designing engineered extracellular matrix for desired cell fates. Conclusion: Molecular dynamics simulation as a non-laboratory tool has many capabilities in providing basic and practical information about the behavior of the molecular components of the cell as well as the interaction of the cell and its components with the surrounding environment. Using this information along with other information obtained from laboratory tools can ultimately lead to the advancement of tissue engineering through the development of more appropriate and efficient methods.

The study of a two-dimensional (2-D) system started nearly half a century ago when Peierls and Landau showed the lack of long range translational order in a two-dimensional solid. In 1968, Mermin proved that despite the absence of long range translational order, two-dimensional solids can still exhibit a different kind of long range bond orientation. During the last decade, fascinating theories were put forward to explain the role of topological defects in the melting of two-dimensional solids, starting with Kosterlitz and Thouless. Recent surge of interest in melting is also due to the theoretical ideas of Halperin, Nelson and Young. They have suggested that the transition may be fundamentally different from that observed in ordinary three-dimensional systems. Computer simulations suggest that the transition is of the usual first-order type observed in a three-dimensional system. A large body of experimental and simulation research into the two-dimensional melting followed the announcement of the KTHNY theory. In spite of all this effort, the question as to the nature of two dimensional melting remains unresolved. Recent experimental work supporting the existence of continuous melting transitions in some two dimensional systems indicates the need for further theoretical and computational work to lead to an understanding of the experimental results.In this paper we intend to summarize and clarify the current situation with regard to research in the two-dimensional melting with an emphasis on computer simulations. The paper begins with an overview of the current status of relevant theoretical, experimental and simulation research, then a two-dimensional simulation of an ionic salt system is studied in detail. This simulation has been done by using the molecular dynamics method. The most important parameters that have been determined are: The transition temperature, the total energy of the system, the mean square displacement and the bond angle distribution. The transition temperature of the system has been specified by plotting some of these parameters as a function of temperature and time. The first order transition is observed. It is difficult to distinguish a hexatic phase from a two-phase coexistence region.

A new molecular dynamics simulation technique for simulating fluids in confinement [H. Eslami, F. Mozaffari, J. Moghadasi, F. Müller-Plathe, J. Chem. Phys. 129 (2008) 194702] is employed to simulate the diffusion coefficient of nanoconfined Lennard-Jones fluid. The diffusing fluid is liquid Ar and the confining surfaces are solid Ar fcc (100) surfaces, which are kept frozen during the simulation. In this simulation just the fluid in confinement is simulated at a constant temperature and a constant parallel component of pressure, which is assumed to be equal to the bulk pressure. It is shown that the calculated parallel (to the surfaces) component of the diffusion coefficients depends on the distance between the surfaces (pore size) and shows oscillatory behavior with respect to the intersurface separations. Our results show that on formation of well-organized layers between the surfaces, the parallel diffusion coefficients decrease considerably with respect to the bulk fluid. The effect of pressure on the parallel diffusion coefficients has also been studied. Better organized layers, and hence, lower diffusion coefficients are observed with increasing the pressure.

In the current research, thermal conductivity of magnetite (Fe3O4) has been calculated using molecular dynamic simulation. The rNEMD Molecular Dynamics Method provided in the LMMPS package is used for the simulation of the thermal conductivity. The effects of magnetite layer size and temperature on the thermal conductivity have been investigated. The numerical results have been validated by experimental data. Results show that the thermal conductivity of magnetite can be predicted appropriately using Buckingham potential function. Moreover, Thermal conductivity of magnetite is shown to be a decreasing function of temperature. The obtained results provide a benchmark for magnetite ferrofluid heat transfer simulations, which has been extensively increased in recent years.