Information Technology Reference
In-Depth Information
implementing programmable and autonomous computing machines with biomole-
cules [39, 3, 32, 38].
14.3 Biomolecular Computing In Silico
Inspired by Adleman's approach and the relatively high cost of molecular proto-
cols, we have developed a computational environment to reproduce in simulation
essentially equivalent chemistry in silico [13, 12]. Software of this type, called vir-
tual test tube (VTT) EdnaCo, was developed to understand biochemical reactions
with DNA oligonucleotides for computational purposes [15]. We next provide a
high-level description of the software involved in the simulation. Further details can
be found in [13]
EdnaCo follows the complex systems paradigm [2] of entities (objects) and in-
teractions, i.e., instead of programming their entire behavior over time; only enti-
ties (originally DNA molecules) and individual interactions between pairs of them
are programmed by the user. Conceptually, the VTT is spatially arranged as a 3D
coordinate system in which molecules can move about. The tube moves molecules
by simulating three different types of motion: Brownian, according to a predeter-
mined schedule, or no motion at all. The entities are allowed to interact freely in
a predetermined manner specified by the experimenter. Entities could be homoge-
nous (all of the same type) or heterogenous (different types) and may represent any
complex biomolecules, herein referred to as DNA complexes. Each molecule is lo-
cated at a unique spatial coordinate at any given time. The VTT can also code for
physical-chemical properties such as temperature, pressure, salinity, and pH that
may vary across space and time and affect the way structures interact therein. Inter-
actions between entities are programmed by the experimenter depending on the na-
ture of the molecules being simulated. Multiple instances of an entity behave in the
same manner as a function of environmental factors such as temperature, pH, and
the like.
All entities are capable of sensing the position of other entities up to a specified
distance defined by a radius of interaction, a parameter in the simulation common
to all entities. If two or more entities come within the interaction distance, an en-
counter is triggered between them. An encounter is resolved by appropriate soft-
ware that may not affect the molecules at all (e.g., DNA molecules may not form a
duplex if the temperature is too high) or may reflect an appropriate chemical reac-
tion (e.g., formation of a DNA duplex and disappearance of the encountering single
strands.) An interaction between two entities may be viewed as a chemical or me-
chanical reaction between them. As a result of an interaction, existing entities may
get consumed, their status may get changed, and/or new entities may, or may not,
get created. Moreover, the concentration of entities may be manipulated externally
by adding or removing entities to or from the VTT at any point of time. The run-
ning time of a simulation is divided into discrete time steps or iterations. At every
iteration, the state of the objects and the tube may change recursively, based on the
Search WWH ::




Custom Search