Energy and charge transfer are the most important phenomena in physics and biology . For example , charge transfer in DNA and charge or energy transfer in photosynthesis are the best examples . Recently , it has been shown that quantum mechanical effects play important role in excitation energy transfer through photosynthetic structures. In this thesis , we briefly review open quantum systems in general and then focus on energy transfer in a linear chain with dipole-dipole interaction . Then , we simulate a toy model for a linear protein structure in different states (ordered , disordered , static and dynamical states) and investigate energy transfer inside the above structure . The simulated protein is a p-loop strand in the selectitivity filter of an ion channel in an excitable cell . In our study , we have investigated the role of noise and dissipation in all states . Our results indicate that system efficiency exponentially decays in terms of dissipation for disordered chain but decays as a power law for ordered chains . On the other side , the effect of noise is constructive for the disordered chain but it is destructive for the ordered chain . As a result , since the linear protein is intrinsically disordered thus the role of noise can be constructive for living systems . Moreover , we have studied the collaborative role of classical and quantum mechanical effect together to see whether the classical effects are stronger than the quantum mechanical effects or not . Our results show that the best efficiency is obtained in equal contributions for both quantum mechanical and classical effects . This type of collaboration can make the functioning of the ion channel more efficient and quicker .