Particle deletion

Mehta and Kofke [91] have recently proposed pseudo-ensemble simulations, in which calculations in a nominal ensemble are mimicked by simulation in a different ensemble or, more precisely, in a pseudo-ensemble. Mehta and Kofke implemented pseudo grand-canonical ensemble simulations in which particle deletion and insertion attempts (pertaining to the constant- uGC constraint in the grand-canonical ensemble) were replaced by volume changes. It has been shown [78] that the approach can be restated as one of attempting to transform a fiVT ensemble into a NPT ensemble such a transformation is possible if the equilibrium pressure Peq corresponding to /tGC can be determined that link can be established by the thermodynamic relationship... 

Boulougouris, G.C. Economou, I.G. Theodorou, D.N. On the calculation of the chemical potential using the particle deletion scheme. Molec. Phys. 1999, 96, 905-913. 

In a dense system, the acceptance rate of particle creation and deletion moves will decrease, and the number of attempts must be correspondingly increased eventually, there will come a point at which grand canonical simulations are not practicable, without some tricks to enliance the sampling. 

In the simplest version, a one-component system is simulated at a given temperature T in both boxes particles in different boxes do not interact directly with each other however, volume moves and particle creation and deletion... 

In some cases, in particular for lattice and polymeric systems, volume change moves may be hard to perform, but particle insertions and deletions may be relatively... 

The acceptance criteria for particle insertion and deletion moves are determined from the detailed balance condition applied to these probabilities. The final expressions are... 

The density dependence of the entropy can also be studied by introducing fluctuations in volume rather than particle number. Typically the particle number approach is favored the computational demands of volume scaling moves scale faster with system size than do addition and deletion moves. Nevertheless, the Wang-Landau approach provides a means for studying volume fluctuations as well. In this case, the excess entropy is determined as a function of volume and potential energy for fixed particle number one, therefore, calculates (V, U). Here the microstate probabilities follow ... 

Fig. 10.12. Vapor-liquid phase behavior for the Lennard-Jones fluid. Solid triangles and hollow squares indicate the results of the particle addition/deletion and volume scaling variants of the flat-histogram simulation using the Wang-Landau algorithm. Crosses are from a histogram reweighting study based on grand-canonical measurements at seven state points. The solid line is from Lotfi, et al. [76], Reprinted figure with permission from [75]. 2002 by the American Physical Society...

These operators are particle-number conserving, that is, action of any excitation operator on an -electron wavefunction (with n arbitrary) leads again to an -electron wavefunction (or deletes it). 

In the presence of tunieamycin, cells infected with Rous sarcoma virus produced virus particles that lacked infectivity, and were devoid of the envelope glycoproteins gp85 and gp35. Virus particles lacking envelope glycoproteins had previously been found in a deletion mutant of Rous sarcoma virus and in a temperature-sensitive mutant of... 

In addition, the polymer-coated adenovirus particles were able to shield against antibody recognition. In another approach, the PEGylation of the adenovirus capsid protein prolonged transgene expression after systemic delivery of El-deleted adenovirus, and allowed partial readministration with native virus (50). Adenovirus has been explored as vector for the treatment of cystic fibrosis (51), for Duchenne muscular dystrophy (52), to deliver tumor suppressor genes for cancer treatment... 

Of the 50 genes present in native X, only about half are necessary for replication in the lytic cycle. Thus, it is possible to delete about 1 / 3 of the genome to make room for more passenger DNA. However, to form mature phage particles the length of the DNA must be at least 75% of the native length. No more than 110% of the native amount may be present. The total DNA must fall between 38 and 53 kb in length. 

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